Top political appointees at Donald Trump’s environment agency are hindering an investigation into the agency’s chief of staff, who pressured a prominent scientist to alter her congressional testimony to make it more favorable for the agency, according to an ethics watchdog.

In the latest development of the fight, the inspector general of the Environmental Protection Agency (EPA) has forced the agency’s head, Andrew Wheeler to explain his position in a letter to Congress. Wheeler’s top agency lawyer is arguing that political staffers have leeway to decide what information to provide to the watchdog, while investigators are warning that agency leaders are trying to subvert their legally mandated independence.

The saga is a striking demonstration of how the Trump administration’s defiance of oversight extends past the impeachment inquiry to include agency watchdogs whose non-partisan reputation has historically put them above the political fray.

Trump’s EPA has removed dozens of science experts from committees meant to offer advice to the government, in some cases replacing them with scientists from conservative states and industry and in others disbanding the groups.

The investigation into the EPA’s chief of staff, Ryan Jackson, revolves around an episode in May 2017, when the agency dismissed the members of the Board of Scientific Counselors, which advises EPA on its research programs.

Deborah Swackhamer, an environmental chemist and retired University of Minnesota professor who led the group, was scheduled to testify to the House science committee on the role of the states in environmental policy two weeks after those dismissals.

But before she could, Jackson obtained her pre-written testimony and asked her to stick to agency “talking points” and play down the dismissals, according to emails reviewed by the New York Times.

Across the federal government, whistleblowers and scientists have said they have been sidelined and silenced by the administration, as Trump seeks to mold science to support his industry-friendly rollbacks of environment and health protections.

The EPA inspector general is now investigating Jackson’s interference in Swackhamer’s testimony, at the request of US lawmakers. In US government, the inspector general office is an independent wing of an agency charged with ensuring against waste, fraud and abuse.

According to emails released by the watchdog, Jackson has refused to say who gave him a copy of Swackhamer’s remarks. For months, he has refused to attend meetings with investigators, who first interviewed him on 24 July. Jackson reportedly left that initial interview before it was complete. He has recently relented and agreed to sit with investigators.

Jackson, who was appointed chief of staff under Wheeler’s predecessor, Scott Pruitt, has been at the center of other agency controversies. Polluters have sought his help when facing fines, according to reporting by E&E News. Under Pruitt’s leadership, Jackson took responsibility for large raises given to Pruitt’s top aides without the consent of Congress.

Jackson previously was chief of staff to the Oklahoma senator James Inhofe, who has vehemently denied climate science, once bringing a snowball to the Senate floor in an attempt to disprove global heating.

In emails with the inspector general’s staff, Jackson has said investigators showed up to his office unannounced and demanded to speak with him. He has criticized them for declining to tell him what specifically they want to discuss.

“The fact that you cannot and will not provide the subject of what you want to meet with me about is unprofessional, and I’m not participating. Unless you have further substantive information, do not contact me further,” Jackson said in an 9 October email.

On 15 October, a top investigator escalated the issue to Wheeler, his deputy and the agency’s top lawyer.

“I am bringing to your attention a matter of deep concern,” said Helina Wong. “As you see from the attached, Chief of Staff Ryan Jackson has – first with delay and now in absolute and final terms – refused to submit to an interview in an ongoing [inspector general] investigation.”

On 21 October, Jackson told another top investigator, Craig Ulmer, that he would only schedule an appointment with him once he knew the topic and had an opportunity to prepare.

“Frankly, I have already met with your staff for an hour. If you would like a second interview send me your questions in writing, and I will respond in writing,” Jackson said.

Finally, on 29 October, the inspector general sent a “seven-day letter”, which is used to report “particularly serious or flagrant problems, abuses or deficiencies”. The letter obligates the agency administrator to send a letter to Congress explaining the situation within a week.

In that letter to Congress, Wheeler said the agency has attempted to “provide reasonable accommodations” to the inspector general. And he backed Jackson’s decision not to identify the person who gave him Swackhamer’s testimony, referring to “constitutional concerns that are ultimately for the Agency and the [inspector general] to resolve”.

But EPA’s top lawyer, Matthew Leopold, has defended Jackson’s previous refusals, saying in a 5 November letter that “it is ultimately the administrator that maintains control of the information sought and decides what constitutes an adequate accommodation by the agency of an OIG request in so far as it is practicable”.

In response, the inspector general’s office says the agency is violating its independence and right to agency information.

In a letter on Thursday, the office said Leopold, “offers free rein to agency staff to refuse [inspector general requests for information”.

Wheeler has maintained that his staffers have done nothing wrong.

“Since the day I joined the agency, it has been my intent to provide [inspector general] with assistance and access to agency information necessary for it to complete its important work, in a manner consistent with the constitution and applicable law,” he said in the letter to Congress. “I believe the agency has provided such assistance in this instance.”