By Katelyn Polantz, Jamie Gangel, Dana Bash and Ella Nilsen

(CNN) — The top criminal prosecutor in the Washington, DC, US Attorney’s Office, Denise Cheung, resigned Tuesday after declining a request from her Trump-appointed superiors to open a grand jury investigation that she viewed as premature, according to multiple people familiar with the matter.

The direction originated from Emil Bove, the department’s acting deputy attorney general, to Ed Martin, whom President Donald Trump has nominated to be the permanent DC US Attorney.

Cheung, a long-time DOJ employee, had been asked to shepherd an investigation into an Environmental Protection Agency funding decision during the Biden administration and then use DOJ’s powers to freeze that funding.

She refused the order and resigned, in part because she believed there wasn’t sufficient evidence to take that step at the time, as well as seeking to protect lower-level prosecutors from the work, source said.

“Earlier yesterday, I was asked to review documentation supplied by the Office of the Deputy Attorney General to open a criminal investigation into whether a contract had been unlawfully awarded by an executive agency before the change in Administration and to issue grand jury subpoenas pursuant to this investigation,” Cheung wrote in a resignation letter to Martin on Tuesday obtained by CNN.

Cheung noted in her letter that she and other experienced white-collar prosecutors looked at whether the DOJ had met its threshold for a grand jury investigation. While Bove’s office insisted that it had, citing a Project Veritas video, Cheung and others didn’t believe the evidence on hand was enough for a grand jury investigation, her letter and additional sources told CNN.

She said after the pushback, the Justice Department instead wanted to freeze assets in a bank related to the Biden-era EPA funding.

The FBI in Washington was looped into DOJ’s plan, and sought legal backup from Cheung. The FBI ultimately wrote to the bank.

Martin, however, criticized that the language in the letter wasn’t explicit enough about a criminal investigation.

“When I explained that the quantum of evidence did not support that action, you stated that you believed that there was sufficient evidence,” Cheung wrote to Martin.

“You also accused me about wasting five hours of the day ‘doing nothing’ except trying to get what the FBI and I wanted, but not what you wanted,” she added.

Cheung made clear to Martin she believed there wasn’t enough probable cause to take the prosecutorial steps Martin demanded.

“Because I believed that I lacked the legal authority to issue such a letter, I told you that I would not do so. You then asked for my resignation,” she wrote, noting the oath of office she took and an obligation to follow legal ethics and the law.

Cheung’s departure revolves around the implementation of stopping some funding from the EPA to non-profit groups.

The Trump administration has consistently criticized Biden’s spending on environmental programs. EPA administrator Lee Zeldin’s said he has had “found” $20 billion worth of funding from former President Joe Biden’s 2022 climate law in a Citibank account, and wanted to return the money to the US Treasury.

The EPA then announced in a press release the EPA would “work with the US Department of Justice” on the matter. CNN has asked EPA for comment.

Cheung didn’t respond to a request for comment from CNN Tuesday morning.

In a statement to CNN, a Justice Department spokesperson said: “Refusing a basic request to pause an investigation so officials can examine the potential waste of government funds is not an act of heroism – just a failure to follow chain of command.”

Zeldin has suggested the funding was rushed to eight non-profits to distribute at the end of the Biden administration through the Inflation Reduction Act, but a former EPA official responsible for implementing the funding told CNN last week it wasn’t rushed or set up nefariously.

EPA had worked with the Treasury Department to set up a financial agent arrangement with Citibank to distribute funding to grantees; it’s the first time EPA has done this type of agreement, but it’s a longstanding process that Treasury has used for years.

Zeldin has taken interest in a Project Veritas video where a Biden-era EPA employee discussed the administration’s climate funding, comparing it to tossing gold bars off the Titanic.

Cheung sent a farewell message office-wide on Tuesday morning. She didn’t publicly indicate her reason for leaving.

Cheung’s departure also comes at a time of roiling change across the DOJ, with prosecutors deemed to be untrustworthy being fired, and ethical clashes erupting between Trump’s hand-picked political appointees and long-time federal prosecutors.

Bove last week presided over a public row with prosecutors in New York and Washington over his order to dismiss charges against New York City Mayor Eric Adams.

Martin, taking the helm of the DC US Attorney’s Office, has supported unwinding all January 6 criminal cases that the office brought. He had enlisted Cheung and another career prosecutor in the office to look at how prosecutors charged January 6 rioters with a felony obstruction charge that the Supreme Court later overturned.

“When I started as an AUSA, I took an oath of office to support and defend the Constitution, and I have executed this duty faithfully during my tenure, which has spanned through numerous Administrations,” Cheung wrote in her sign-off email to her colleagues. “I know that all of the AUSAs in the office continue to honor their oaths on a daily basis, just as I know that you have always conducted yourself with the utmost integrity.”

CNN’s Hannah Rabinowitz contributed to this report.

This story has been updated with additional details.

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