Home Secretary Theresa May has said she stands by her comments about a decision to relax some UK border checks - which have been denied by a senior official.
In a rowdy Commons debate, she attacked Labour's record on immigration and said her pilot scheme was aimed at "strengthening our borders".
Labour's Yvette Cooper accused her of not knowing where the scheme was in place or what the security risks were.
Former borders chief Brodie Clark says Mrs May's account of events is "wrong".
He was suspended last week by UK Border Agency chief Rob Whiteman, who says Mr Clark admitted authorising staff on a number of occasions to go beyond ministerial instructions.
Mrs May says she authorised the relaxation of some checks on children from the EU travelling in groups and on biometric passports of EU citizens under "limited circumstances" at peak times - but claims Mr Clark allowed officials to go further, without ministerial approval.
In the Labour-led debate on Wednesday, three former Labour home secretaries - David Blunkett, Jack Straw and Alan Johnson - criticised Mrs May, with Mr Johnson saying the treatment of Brodie Clark had been "reprehensible" and predicting he would win an employment tribunal.
Shadow home secretary Ms Cooper accused Mrs May of a "deafening silence" on questions about the numbers of people let through under the pilot scheme - and the exact nature of instructions from the Home Office to the UK Border Agency.
She said an instruction to border staff showed that the home secretary's intention and policy had been "to expand the reduction of checks on EEA citizens across the country".
"That operational instruction says: 'We will cease routinely opening the chip in EEA passports... if that was government policy, it's little wonder that across the country people have been routinely stopping the biometric checks in EU passports and stopping the watch index checks."
She said the real reason for the policy was that border staff had been cut by 1,500, making it impossible for staff to carry out advanced checks and keep queues down: "People across the country now fear that corners are being cut and border security is being put at risk by the scale of the government's border cuts as well."
But Conservative backbenchers repeatedly attacked Labour's record on immigration. And Mrs May, who was joined by Immigration Minister Damian Green on the front bench, said her pilot scheme had been aimed at strengthening border security by allowing officials the discretion to focus on "high risk" passengers.
"My pilot did not in any way put border security at risk, that is my assessment and it is the assessment of UK Border Agency."
She questioned Mr Clark's statement, in which he argued that some of the measures implemented had been in place since 2008-9. Mrs May said, if he was talking about the warnings index guidance "it does not permit the extent of the relaxations allowed".
She added: "I stand by every word I have told the House on Monday, yesterday and again today."
Mr Green responded to claims that he authorised an extension of the pilot programme by saying: "I am happy to tell the house that I didn't."
Earlier Labour leader Ed Miliband said the row had turned into a "complete fiasco" - but David Cameron said he "fully backs" Mrs May over her pilot scheme which he said led to a 100% increase in firearms seizures.
Mr Clark stepped down as head of the UK Border Force on Tuesday saying he would lodge a claim for constructive dismissal and that Mrs May's remarks had made his position "untenable".
He added: "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."
He is expected to face questions from MPs on the Home Affairs Select Committee next week. The BBC understands that Damian Green, who will also give evidence to the committee, is likely to maintain he had not been aware that officials had gone beyond the home secretary's instructions on the pilot scheme until last week.
Jonathan Baume, from the FDA trade union which represents senior civil servants, said the home secretary had spent two days "traducing" and "damning" Mr Clark - without giving him the chance to give his side of the story. He 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 - which is due to report in January.
Chief executive of the UK Border 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.