Defense secretary says Pentagon official who questioned legality of withholding Ukraine aid to resign

Deputy Under Secretary of Defense (Comptroller) Elaine McCusker will resign effective June 26, Esper said in a statement.

"Since joining the Department of Defense Elaine has worked tirelessly to ensure that our budgeting and audit processes give full value to the taxpayer while meeting the enormous security needs of our nation as well as the men and women who serve it," Esper said. "I am grateful for her dedication to public service and the contributions that she has made to the Department and wish her the very best in her future endeavors."

In March, CNN reported that the White House was withdrawing the nomination of McCusker to be the Pentagon's comptroller. She had served as the acting official in that role and last year, raised concerns about the legality of Ukraine military aid being held by the Trump administration, an issue that ultimately led to President Donald Trump being impeached.

McCusker's name -- and qualms about the aid -- have appeared in correspondence between government officials.

CNN previously reported that on September 5, McCusker mentioned the "increasing risk of execution," a nod to concerns at the Pentagon that continuing the hold could prevent all the money from being spent.

Finally, on the evening of September 11, Michael Duffey, associate director of national security programs at the Office of Management and Budget, alerted McCusker that he was releasing the money for Ukraine.

"Copy. What happened?" McCusker asked.

The first line of Duffey's response is redacted. He went on to say he hoped to sign the apportionment to release the money that evening and signed off, "Glad to have this behind us."

McCusker first raised concerns about the legality of the hold on July 25, according to emails viewed and reported on earlier this year by Just Security, a website focusing on reporting and analysis of national security law and policy. That was the same day as Trump's now infamous call with his Ukrainian counterpart Volodymyr Zelensky, in which the President pressed Zelensky for investigations that could boost him politically.

Just Security also reviewed an August 30 email from Duffey to McCusker stating the freeze on aid to Ukraine would continue at the explicit direction of the President despite growing legal concerns within the Pentagon and mounting external questions prompted by news of the hold becoming public just days prior.

The documents highlight McCusker's concerns that OMB was not representing the Pentagon's concerns accurately.

"Recognizing the importance of decision space, but this situation is really unworkable made particularly difficult because OMB lawyers continue to consistently mischaracterize the process — and the information we have provided. They keep repeating that this pause will not impact DOD's ability to execute on time," McCusker wrote to Esper's chief of staff on August 27 in response to an inquiry about the hold from a defense contractor.

When Duffey suggested in a September 9 email to McCusker that the Pentagon, not OMB, would be to blame if the money was not spent, McCusker wrote: "You can't be serious. I am speechless."

A senior administration official told CNN in January that OMB officials believed that McCusker was exaggerating the numbers about the money that the Pentagon would be unable to spend if the hold wasn't lifted. The official also claimed there were other top Defense Department officials who disagreed with McCusker's conclusions.

McCusker was not the first White House nominee to have her offer rescinded. Earlier this month, Trump abruptly withdrew a Treasury Department nomination for Jessie Liu, the former US attorney who headed the office that oversaw Roger Stone's prosecution -- a decision that was directly tied to her former job, CNN learned. Liu resigned shortly after.

This story has been updated with additional information.