A former military adviser who worked for Hillary Clinton at the State Department says her “sloppy communications with her senior staff” could have undermined two counterterrorism operations.

Bill Johnson, the department’s adviser to the special operations section of the US Pacific Command in 2010 and 2011, told Newsweek that secret plans to kill the head of a Filipino jihadi group and stop Chinese armaments being smuggled into Iraq both failed.

“I had several missions that went inexplicably wrong, with the targets one step ahead of us,” said Johnson, who worked in Air Force special ops for more than 25 years before joining the State Department in 1999.

He said investigations narrowed down the source of potential leaks to Clinton’s and her aides’ use of unprotected phones — although he admitted he had no solid proof.

In the Philippines, his team targeted Umbra Jumdail, founder of the Abu Sayyaf jihadist group.

“We had good intel. We knew where he was,” Johnson said. “He would be gone three hours before, sometimes as little as a half-hour before. We knew he was getting tipped off somehow.”

Johnson came to believe that unsecure chatter between Clinton staffers in DC and the US Embassy in Manila was to blame.

“Anyone can just sit outside the embassy and listen” with eavesdropping devices, he said. “We suspected the leaks [came from] somewhere at State at the time.”

He said his team stopped warning top State officials about raids, and in February 2012, Jumdail was killed in a US-backed airstrike.

The allegations came a day after a State Department inspector general’s report criticized her use of a private email server.

Clinton has dismissed the IG’s findings as “the same story,” and noted that previous secretaries of state used personal email.

Her spokesman Nick Merrill called Johnson’s allegations “patently false.”

Donald Trump weighed in on the email flap on Thursday.

“This is all bad judgment, probably illegal. We’ll have to find out what the FBI says about it,” he said in Bismarck, ND.