Theresa May is under pressure to explain her decision to relax some border checks, after a senior official accused her of misleading Parliament.
UK Border Force chief Brodie Clark stepped down on Tuesday saying Mrs May's claim that he had gone further than ministers authorised was "wrong".
MPs will debate the row later as Labour demand more details of Home Office guidance given to the UK Border Agency.
Labour's Yvette Cooper said the row was "sapping confidence" in Mrs May.
'Serious answers'
Mrs May says that she had allowed some checks on European travellers to be relaxed for a four-month period from July, but said Mr Clark went further in scaling back checks - including on people from outside the European Economic Area - without her approval. He was suspended last week.
But in a statement released on Tuesday evening, Mr Clark stepped down, saying he would lodge a claim for constructive dismissal and that Mrs May's remarks had made his position "untenable".
"Those statements are wrong and were made without the benefit of hearing my response to formal allegations... the home secretary suggests that I added additional measures, improperly, to the trial of our risk-based controls. I did not. Those measures have been in place since 2008/09.
"The home secretary also implies that I relaxed the controls in favour of queue management. I did not. Despite pressure to reduce queues, including from ministers, I can never be accused of compromising security for convenience."
Shadow home secretary Yvette Cooper told the BBC the two versions of events were "contradictory".
"Security breaches took place this summer. We know she's undermined the checks, but she hasn't revealed the full truth. We've got an escalating fiasco in which you have a contradictory story between her and her most senior official," Ms Cooper said.
"If she doesn't tell the truth today and publish all of the data, publish all of the information that she gave to the Borders Agency, then we are going to see a continual sapping of the home secretary's authority."
Later MPs will debate a Labour motion calling on the government to "publish immediately" the details Mrs May and Immigration Minister Damian Green gave to the UKBA, which oversees the operation of the UK Border Force at airports and ports.
The motion also asks whether they signed off operational instructions giving the UKBA greater flexibility.
Mrs May told MPs on Tuesday that she had not informed cabinet of her decision as the "limited" pilot was an "operational matter" which "did not in any way put border security at risk" and said she would not resign over the revelations.
Accusing Mr Clark of "unauthorised" actions, she said: "I take full responsibility for my decisions and actions related to the pilot, but Brodie Clark must take responsibility for his actions."
Jonathan Baume, from the First Division Association, the trade union which represents senior civil servants, said Mr Clark had been willing to answer the issues raised internally.
"But instead he was suspended and the home secretary has spent two days basically traducing him and damning him without ever giving the civil servant the opportunity to present their case."
Mr Clark - one of three UKBA officials suspended last week - is due to give evidence to the home affairs select committee next week.
Mrs May has announced there will be three inquiries, the main one led by the Chief Inspector of the UK Border Agency, John Vine.
Chief executive of the UK Borders Agency Rob Whiteman said he had suspended Mr Clark after he had admitted last week to authorising staff to go further than ministerial instruction, on a number of occasions.
"In my opinion it was right for officials to have recommended the pilot so that we focus attention on higher risks to our border, but it is unacceptable that one of my senior officials
Source: BBC NEWS