Malley kept doing State Department work for weeks after his clearance was suspended, taking phone calls and fielding media interviews.

When lawmakers noticed his absence from a key Congressional Iran briefing, State officials indicated that he was taking leave for reasons unrelated to his government work. But as CNN broke the news that Malley’s security clearance had been suspended, the State Department announced that he had been put on full, unpaid leave and that his deputy had stepped in as acting special envoy for Iran.

Republicans are now calling for an investigation into the saga. Hagerty, the top Republican on the Foreign Relations Committee panel that oversees the State Department, wrote in the letter that its signatories were “alarmed” to learn that Malley could have mishandled classified information.

In the letter, Hagerty and others posed a host of questions to the head of the Inspector General’s Office. The queries highlight just how little is known about Malley’s mysterious departure from the State Department:

When was he notified in writing that his clearance had been suspended, as required by the State Department’s manual? When were the actions that led to the suspension? Did he lose physical access to the highly-secured area around the secretary of State’s office? When were members of Malley’s team ordered to stop sharing classified information with him? Why wasn’t he put on unpaid leave as soon as his clearance was suspended?

The letter also homes in on a challenge the department may soon face: replacing Malley. Last year’s National Defense Authorization Act included a requirement — pushed for by Sen. Jim Risch (R-Idaho), the top Republican on the Senate Foreign Relations Committee — that diplomats in Malley’s role secure Senate confirmation. Malley took the job before that requirement became law. But now, his successor is subject to it.

The letter also signals that Republicans believe the State Department may have broken that law when Abram Paley took over as acting special envoy for Iran. Is Paley “exercising significant authority pursuant to the laws of the United States?” it asks. It also noted that Paley’s assignment would have required certain notifications be sent to relevant congressional committees and asked whether that was done.

A spokesperson for Senate Foreign Relations Chair Bob Menendez declined to comment on whether or not his office received any notice of Paley’s new role. And a spokesperson for Hagerty said the senator is unaware of any notification reaching the panel. State Department spokesperson Matthew Miller declined to comment on communications with Congress about Paley’s role.

Secretary of State Antony Blinken defended Malley in an interview with MSNBC this week, saying he has served the U.S. admirably. The two men have been friends for decades.

Sen. Chris Van Hollen (D-Md.), a member of the Senate Foreign Relations Committee, has also come to Malley’s defense, saying: “I’ve always known him to be someone who’s very careful when it comes to America’s secrets.”

Hagerty called Malley’s situation troubling.

“I’m deeply concerned,” he said in an interview, “and I think every American should be deeply concerned about what’s going on with Malley.”

Nahal Toosi contributed reporting.