Tony Blair is standing by Stephen Byers despite a statement from the transport department's top civil servant indicating that Martin Sixsmith did not voluntarily resign.

The statement will provoke renewed claims that Byers lied over his involvement in the dismissal of Sixsmith, the transport department's communications chief.

In what is fast dissolving into a row of semantics, the government continued to defend itself against cover-up allegations over the weekend, after Sixsmith denied claims that he had resigned from his post as communications director at the Department for Transport, Local Government and the Regions.

Speaking on Monday, Downing Street insisted it was standing by the minister. "The prime minister has full confidence in Stephen Byers," said a Number 10 spokesman.

Sir Richard Mottram's statement

But a statement issued by Sir Richard Mottram, the permanent secretary at the DTLR, confirmed that Sixsmith had not agreed to the terms of his resignation at the time news of his departure was first leaked to the media, and subsequently confirmed in media interviews by Byers.

"On Friday 15 February, it was clear to me that this situation could not continue and that Jo Moore and Martin Sixsmith should both leave their posts, because relationships within the department and with its ministers had broken down. I discussed this with Mr Byers. He agreed with my proposal. We agreed he would talk to Jo Moore and I would talk to Mr Sixsmith," said the statement.

In his meeting with Sir Richard, Sixsmith was "reluctant" to resign, but agreed on the conditions that Jo Moore also resigned, that the terms of the resignation did not blame him, and that financial terms were also agreed.

"We agreed to meet again to discuss his other conditions after a long-standing hospital appointment which he wished to fulfil. It was envisaged that his resignation and that of Jo Moore would be announced later that afternoon...At this stage I informed the secretary of state and the cabinet secretary that Mr Sixsmith had agreed to resign."

When the news leaked, and because Sixsmith was late returning from his hospital appointment, the resignations were then confirmed.

"I met Mr Sixsmith at 5.30pm that evening. At that meeting he argued that he had never resigned. He said that the release of the announcement without his agreement changed everything," said Sir Richard.

The statement said discussions on settlement terms had continued, and that the department "still stands ready to discuss with him the terms of his departure".

The statement appears to back Sixsmith's version of events that the terms of his resignation had not been agreed at the time it was publicly announced, although the department will point out that the announcement met with the terms Sixsmith set out, including the resignation of Moore and the absence of blame for any misconduct.

Resignation calls

Opposition calls for Byers' resignation intensified on Monday as the row deepened.

Conservative leader Iain Duncan Smith said Byers had "clearly lost control".

"If he can't get a grip of his own staff how is he ever going to get to grips with the rail network? He should go and go now."

He said that Britain needed an impartial civil service that was able to work with any party without fear or favour.

"Political advisers are clearly stopping them from doing that. We need to write the neutrality of the civil service into law to put officials beyond the reach of bullying by spin doctors.

"If Labour won't stand up for good government, we will," said Duncan Smith.

Charles Kennedy, the Lib Dem leader, said the minister should stand aside. "It's all pretty unedifying stuff," he said. "The transport department is unable to operate efficiently in present circumstances. I can't see how Stephen Byers can run the show when he's distracted to this degree.

"It's office politics which has reached a gigantic level when it's in the headlines day after day. I don't think Stephen Byers has got much option but to resign and let someone else pick up the reigns."

Byers made no comment on the growing crisis as he flew to Heathrow to return to his department after last week's recess.

He later passed a resignation-hungry media scrum as he arrived at his department in a chauffeur-driven Rover.

Pressure mounts

The pressure mounted on the government over the weekend after Sixsmith claimed he had not resigned.

In an explosive rebuff to Byers, Sixsmith said: "I wasn't sacked, I didn't resign, I haven't offered my resignation. Stephen Byers wanted me to resign because he said he would only accept Jo Moore's resignation if I resigned at the same time."

Sixsmith claimed that the permanent secretary at the department, Sir Richard Mottram, had assured him he would not be forced out of his job.

"Very senior people, including ministers, MPs, journalists and union officials found themselves being misled into providing on-the-record reaction to this false story," he said. "Why did this all happen? Because Stephen Byers had said so."

Contradictory evidence

Earlier on Monday, Downing Street had given its full backing to Byers.

The intervention came after Byers denied that he had insisted on Sixsmith's resignation as the quid pro quo for the dismissal of his special adviser Jo Moore.

The resignation, along with that of spin doctor Moore, was announced on February 15 following reports that Moore had sought to publish damaging rail statistics on the same day as the funeral of Princess Margaret.

However, Byers categorically denied the claims - suggesting he made no comment on personnel issues within the department.

"Martin Sixsmith agreed with Sir Richard Mottram, the permanent secretary, that he, Martin Sixsmith, would resign from his post as director of communications on February 15. That's the situation which is agreed and stated by Sir Richard Mottram. Those are the facts," he said.

The Scottish secretary, Helen Liddell, said she did not believe that Byers had intentionally misled anyone.

"Stephen is a straightforward man who went on information from the permanent secretary, who had been told that Martin Sixsmith had resigned and that part of that was that Jo Moore should go as well," she told the BBC's Breakfast With Frost.