The FBI and the State Department are at odds over whether Hillary Clinton’s personal lawyers had the proper government-issued security clearances that they needed to keep copies of her emails in a Washington, D.C., law office last year.

Some of those emails contained classified information, which the lawyers and State Department officials knew at the time.

The issue has become a flashpoint in the broader controversy over Clinton’s private email server. Republican lawmakers are pressing the FBI on whether it investigated the State Department’s decision to give security clearances to Clinton’s attorneys and let them store copies of the emails on a thumb drive. And statements from FBI and State Department officials show that there’s no clear agreement on whether Clinton’s attorneys were appropriately cleared to handle the material.

In July, FBI Director James Comey testified before the House Oversight and Government Reform that Clinton’s attorneys didn’t have the security clearances they needed. The FBI elaborated in a statement this week to The Daily Beast, saying “most of the attorneys representing former Secretary of State Clinton in this matter did not have the appropriate security clearances to review special access program material,” which is highly secret information that is restricted only to a few people based on their need to know.

Seven email chains, which included messages sent and received by Clinton, contained such material, the FBI found.

The bureau didn’t specify which lawyers didn’t have the right clearances, but Clinton has been represented by at least two lawyers in matters related to her email, including her longtime personal attorney, David Kendall, of Williams & Connolly, and his colleague, Katherine Turner.

Kendall, who has previously said he and Turner hold a top secret clearance from the State Department, didn’t respond to a request for comment.

But the State Department says Clinton was represented by appropriately cleared lawyers. A department spokesperson defended the decision in 2015 to let the attorneys keep the thumb drive in a government-issue safe, which department security officers provided after visiting Williams & Connolly’s offices. At the time, Clinton’s lawyers said they needed a full record of the emails in order to respond to questions from the House committee investigating the Benghazi, Libya, terrorist attacks, which happened on Clinton’s watch.

“It’s routine for individuals outside government to have temporary security clearances to work on a range of issues,” State Department spokesperson Elizabeth Trudeau told The Daily Beast. “This includes legal representatives who may need it to better represent their clients appropriately. The Department does not confirm individuals’ security clearance status, however, as we have confirmed in the past, former Secretary Clinton has counsel with clearance.”

While Clinton’s lawyers won’t face any criminal prosecution over the issue, legal and security experts say giving them access to classified emails in their own offices was an unorthodox decision that appeared to give preferential treatment to the former secretary of state. Keeping classified information stored outside a government facility increases the possibility that it could be seen or stolen by people who aren’t authorized to have it.

Rep. Jason Chaffetz, the chairman of the powerful House Oversight Committee, held Clinton personally responsible for the matter.

“Hillary Clinton gave her private attorneys, without proper security clearance, access to classified information. This once again illustrates Secretary Clinton’s cavalier and sloppy behavior in handling highly sensitive information,” Chaffetz told The Daily Beast. Last week, Chaffetz asked Comey in writing whether law enforcement officials had “investigated the possibility that Secretary Clinton’s classified emails were improperly stored or accessed” either by her “personal representatives” or her attorneys.

The issue is complicated by the fact that not all classified government information is treated the same. There are three ascending levels of classification: confidential, secret, and top secret. Clinton’s emails contained information in all three categories.

But her lawyers learned about classified information in the emails at different times. First, they were informed in May 2015 by the State Department that at least one email contained “secret” information. At the time, State decided to install the safe at Williams & Connolly’s offices.

Then, in June 2015, the State Department told the lawyers that 25 emails contained “confidential” information. That’s a lower level than secret, and department security officers had determined that the safe and the law office were appropriate for handling information up to the secret level.

But in July, the inspectors general for the State Department and the intelligence community said they’d found four emails that contained information derived from intelligence agencies. That signaled that the emails could contain information from the most highly-classified category, and the law offices weren’t set up to handle those sensitive secrets.

“We knew nothing about the clearances for counsel or for the law firm,” Charles McCullough, the inspector general for the intelligence agencies, told Congress last month. “I was facing a situation where I had classified information, it appeared to me, outside the care, custody, and control of the U.S. government.”

After the inspectors general discovered the classified information, intelligence agencies and the State Department would spend the next several months arguing over precisely how many of Clinton’s emails contained which category of secrets. And internal emails obtained by The Daily Beast under the Freedom of Information Act show that in late July and early August of 2015, State Department lawyers were trying to determine whether attorneys representing Clinton had the clearances they needed.

The question was pressing enough that a State Department legal adviser sent several emails marked “URGENT” to the security officers who had been in charge of vetting Clinton’s attorneys’ offices and setting up the safe.

“Do any of the attorneys have TS [top secret] clearances?” the adviser, Sarah Prosser, wrote, apparently not knowing the answer. The replies from her colleagues are heavily redacted, but the exchanges make clear that State’s attorneys tried to sort out the issue at a critical time.

On the same day Prosser sent the message, the FBI took possession of the thumb drive from Clinton’s lawyers. They would no longer be allowed to keep the emails in their office.

In its statement to The Daily Beast, the FBI seemed to absolve Clinton’s attorneys of any responsibility for knowing what was in the emails. “The FBI does not believe the lawyers knew, or should have known at the time, that there was classified information in her emails,” the statement read.

But clearly the lawyers did know that the emails contained confidential and secret information, because they were told so by State Department officials. Asked to clarify which levels of classification the lawyers did or didn’t know about, an FBI spokesperson declined further comment.

But in the end, it was the responsibility of the State Department to ensure that the lawyers were properly vetted and their firm was prepared to handle classified information. And, the department says, its staff did just that.

The decision to give the attorneys a safe was approved by the State Department’s Diplomatic Security Bureau, “taking into account all relevant factors including security clearances and access controls,” Trudeau said. State also provided “instructions for how to secure the material (up to the secret level of classification),” the second-highest of the three basic classification levels the government uses.

“Through a physical security expert, we confirmed that they were taking those measures,” Trudeau continued. “The Department also informed counsel that additional steps would be required if the Department determined the material contained more highly classified information.”

That ultimately proved unnecessary because the FBI came in August and took the thumb drive. At the time, investigators also seized Clinton’s private server. In going through those records, investigators determined that Clinton’s lawyers hadn’t actually read all her emails when they tried to sort out which ones were work-related—the ones that ended up on the thumb drive—and which ones were personal. The lawyers deleted those.

Last week, the FBI revealed that investigators have found another 15,000 emails that Clinton’s attorneys never turned over. It’s not clear how many of those involved official communications, and the FBI has said there’s no evidence the lawyers intentionally withheld the messages. But the revelation has only added to Republican suspicions that Clinton—and her attorneys—haven’t told the full story about her email.