At the center of a criminal probe involving Hillary Clinton’s handling of classified information is a series of emails between American diplomats in Islamabad and their superiors in Washington about whether to oppose specific drone strikes in Pakistan.
The 2011 and 2012 emails were sent via the “low side’’—government slang for a computer system for unclassified matters—as part of a secret arrangement that gave the State Department more of a voice in whether a Central Intelligence Agency drone strike went ahead, according to congressional and law-enforcement officials briefed on the Federal Bureau of Investigation probe.
Some of the emails were then forwarded by Mrs. Clinton’s aides to her personal email account, which routed them to a server she kept at her home in suburban New York when she was secretary of state, the officials said. Investigators have raised concerns that Mrs. Clinton’s personal server was less secure than State Department systems.
The vaguely worded messages didn’t mention the “CIA,” “drones” or details about the militant targets, officials said.
The still-secret emails are a key part of the FBI investigation that has long dogged Mrs. Clinton’s campaign, these officials said.
They were written within the often-narrow time frame in which State Department officials had to decide whether or not to object to drone strikes before the CIA pulled the trigger, the officials said.
Law-enforcement and intelligence officials said State Department deliberations about the covert CIA drone program should have been conducted over a more secure government computer system designed to handle classified information.
State Department officials told FBI investigators they communicated via the less-secure system on a few instances, according to congressional and law-enforcement officials. It happened when decisions about imminent strikes had to be relayed fast and the U.S. diplomats in Pakistan or Washington didn’t have ready access to a more-secure system, either because it was night or they were traveling.
Emails sent over the low side sometimes were informal discussions that occurred in addition to more-formal notifications through secure communications, the officials said.
One such exchange came just before Christmas in 2011, when the U.S. ambassador sent a short, cryptic note to his boss indicating a drone strike was planned. That sparked a back-and-forth among Mrs. Clinton’s senior advisers over the next few days, in which it was clear they were having the discussions in part because people were away from their offices for the holiday and didn’t have access to a classified computer, officials said.
The CIA drone campaign, though widely reported in Pakistan, is treated as secret by the U.S. government. Under strict U.S. classification rules, U.S. officials have been barred from discussing strikes publicly and even privately outside of secure communications systems.
The State Department said in January that 22 emails on Mrs. Clinton’s personal server at her home have been judged to contain top-secret information and aren’t being publicly released. Many of them dealt with whether diplomats concurred or not with the CIA drone strikes, congressional and law-enforcement officials said.
Several law-enforcement officials said they don’t expect any criminal charges to be filed as a result of the investigation, although a final review of the evidence will be made only after an expected FBI interview with Mrs. Clinton this summer.
One reason is that government workers at several agencies, including the departments of Defense, Justice and State, have occasionally resorted to the low-side system to give each other notice about sensitive but fast-moving events, according to one law-enforcement official.
When Mrs. Clinton has been asked about the possibility of being criminally charged over the email issue, she has repeatedly said “that is not going to happen.’’ She has said it was a mistake to use a personal server for email but it was a decision she made as a matter of convenience.
Clinton campaign spokesman Brian Fallon said: “If these officials’ descriptions are true, these emails were originated by career diplomats, and the sending of these types of emails was widespread within the government.”
U.S. officials said there is no evidence Pakistani intelligence officials intercepted any of the low-side State Department emails or used them to protect militants.
State Department spokesman Mark Toner said the agency “is not going to speak to the content of documents, nor would we speak to any ongoing review.’’
The email issue has dogged Mrs. Clintonfor more than a year. Despite her success in nailing down the Democratic presidential nomination, polls show many voters continue to doubt her truthfulness and integrity. Her campaign manager has acknowledged the email matter has hurt her.
Republican rival Donald Trump has attacked Mrs. Clinton repeatedly on the issue, calling her “Crooked Hillary,’’ saying what she did was a crime and suggesting the Justice Department would let her off because it is run by Democrats.
Beyond the campaign implications, the investigation exposes the latest chapter in a power struggle that pits the enforcers of strict secrecy, including the FBI and CIA, against some officials at the State Department and other agencies who want a greater voice in the use of covert lethal force around the globe, because of the impact it has on broader U.S. policy goals.
In the case of Pakistan, U.S. diplomats found themselves in a difficult position.
Despite being treated as top secret by the CIA, the drone program has long been in the public domain in Pakistan. Television stations there go live with reports of each strike, undermining U.S. efforts to foster goodwill and cooperation against militants through billions of dollars in American aid.
Pakistani officials, while publicly opposing the drone program, secretly consented to the CIA campaign by clearing airspace in the militant-dense tribal areas along the Afghan border, according to former U.S. and Pakistani officials.
CIA and White House officials credit a sharp ramp-up in drone strikes early in Mr. Obama’s presidency with battering al Qaeda’s leadership in the Pakistani tribal areas and helping protect U.S. forces next door in Afghanistan. Targets have also included some of the Pakistan government’s militant enemies.
In 2011, Pakistani officials began to push back in private against the drone program, raising questions for the U.S. over the extent to which the program still had their consent.
U.S. diplomats warned the CIA and White House they risked losing access to Pakistan’s airspace unless more discretion was shown, said current and former officials. Within the administration, State Department and military officials argued that the CIA needed to be more “judicious” about when strikes were launched. They weren’t challenging the spy agency’s specific choice of targets, but mainly the timing of strikes.
The CIA initially chafed at the idea of giving the State Department more of a voice in the process. Under a compromise reached around the year 2011, CIA officers would notify their embassy counterparts in Islamabad when a strike in Pakistan was planned, so then-U.S. ambassador Cameron Munter or another senior diplomat could decide whether to “concur” or “non-concur.” Mr. Munter declined to comment.
Diplomats in Islamabad would communicate the decision to their superiors in Washington. A main purpose was to give then-Secretary of State Clinton and her top aides a chance to consider whether she wanted to weigh in with the CIA director about a planned strike.
With the compromise, State Department-CIA tensions began to subside. Only once or twice during Mrs. Clinton’s tenure at State did U.S. diplomats object to a planned CIA strike, according to congressional and law-enforcement officials familiar with the emails.
U.S. diplomats in Pakistan and Washington usually relayed and discussed their concur or non-concur decisions via the State Department’s more-secure messaging system. But about a half-dozen times, when they were away from more-secure equipment, they improvised by sending emails on their smartphones about whether they backed an impending strike or not, the officials said.
The time available to the State Department to weigh in on a planned strike varied widely, from several days to as little as 20 or 30 minutes. “If a strike was imminent, it was futile to use the high side, which no one would see for seven hours,” said one official.
Adding to those communications hurdles, U.S. intelligence officials privately objected to the State Department even using its high-side system. They wanted diplomats to use a still-more-secure system called the Joint Worldwide Intelligence Community Systems, or JWICs. State Department officials don’t have ready access to that system, even in Washington. If drone-strike decisions were needed quickly, it wouldn’t be an option, officials said.
Some officials chafed at pressure to send internal deliberations through intelligence channels, since they were discussing whether to push back against the CIA, congressional officials said.
The Wall Street Journal first reported on the State Department-CIAtug-of-war over the drone program in 2011.
Under pressure to address critics abroad, Mr. Obama pledged to increase the transparency of drone operations by shifting, as much as possible, control of drone programs around the world to the U.S. military instead of the CIA. An exception was made for Pakistan.
But even in Pakistan, Mr. Obama recently signaled a shift. The drone strike that killed Taliban leader Mullah Akhtar Mansour last month was conducted by the military, not the CIA, and the outcome was disclosed.
While the CIA still controls drones over the tribal areas of Pakistan near Afghanistan, the pace of strikes has declined dramatically in recent years. U.S. officials say there are fewer al Qaeda targets there now that the CIA can find.
Write to Adam Entous at adam.entous@wsj.com and Devlin Barrett at devlin.barrett@wsj.com
