Brodie Clark, the suspended senior civil servant at the centre of the border checks row, has quit his job as head of the UK border force, and openly attacked the home secretary for making him a scapegoat for her political convenience.

Clark, who said he is lodging a claim for constructive dismissal, flatly denied Theresa May's charge that he had improperly relaxed passport checks at Britain's borders in order to manage growing airport queues.

The decision by such a senior civil servant, who has 40 years' experience of running Britain's prisons and immigration services, to openly denounce the home secretary will put her position under renewed pressure.

May faces a renewed Commons confrontation on Wednesday over the fiasco for the third day running when Labour mounts an opposition-day debate on the affair.

Clark's decision to break his silence revives memories of the famous 1990s clash when Michael Howard sacked his prison boss, Derek Lewis, in a dispute over the boundary between operational and policy matters. Clark said he deeply regretted having to make the statement: "I am saddened that my career should end in such a way after 40 years' dedicated service. My employer has disregarded my right of reply in favour of political convenience."

The senior civil servant rose to prominence when he was the governor of Whitemoor maximum security prison at the time of a breakout by IRA men in 1994. Clark has handled some of the most difficult operational jobs inside the Home Office, including managing the immigration detention estate at the time of the Yarl's Wood fire.

He claimed that while he faced pressure to reduce airport queues, including from ministers, he could never be accused of compromising security for convenience.

"This summer saw queues of over three hours (non EU) on a regular basis at Heathrow and I never once contemplated cutting our essential controls to ease the flow," he said in a statement issued via his union, the First Division Association.

He said his position had been made untenable by May's repeated assertions thathe had been at fault and her renewed allegations before the Commons home affairs select committee on Tuesday: "Those statements were wrong and were made without the benefit of hearing my response to formal allegations. With the home secretary announcing and repeating her view that I am at fault, I cannot see how any process conducted by the Home Office, or under its auspices, can be fair and balanced."

He said that the home secretary had accused him of improperly taking additional measures beyond those agreed in July for the month-long trial of risk-based passport checks: "I did not. Those measures have been in place since 2008/09," he said.

Downing Street sources made clear on Tuesday night that there was no change in the prime minister's position on May after the resignation of Clark. Sources said the prime minister remained supportive of the home secretary.