Brodie Clark was suspended by the Home Secretary Theresa May last week after being accused of relaxing immigration controls beyond what she had asked for.
He now plans to lodge a claim for “constructive dismissal”, and has denied acting improperly.
Earlier, Mrs May said he must “take full responsibility for his actions”.
The home secretary allowed some checks on European travellers to be relaxed, but says Mr Clark went further in scaling back checks, without her approval.
In a statement, Mr Clark said his position at the UK Borders Agency had been made “untenable” because of the statements made in the House of Commons by Mrs May.
“Those statements are wrong and were made without the benefit of hearing my response to formal allegations,” he said.
“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.
“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 he was saddened his career should end in this way after 40 years of “dedicated service”, and regretted Mrs May had “disregarded my right to reply” in favour of political convenience.
Mr Clark – one of three UKBA officials suspended last week – is due to give evidence to the home affairs select committee next week.
Earlier, Mrs May faced questions from that committee about her involvement in a pilot scheme.
She told MPs she had not told the Cabinet of her decision to allow officials to relax checks on some European travellers arriving in the UK as the “limited” pilot was an “operational matter” which “did not in any way put border security at risk”.
She said the idea was that at busy times it was safer to carry out “intelligence-led” checks on suspicious passengers rather than mandatory checks on all passengers, including those who were “low risk”.
Labour committee member David Winnick suggested ministers should take full responsibility for a “major blunder” on their watch and asked if there was any question of Mrs May resigning – to which the home secretary responded: “No.”
She added that she would take responsibility for the authorised pilot, which she suggested had led to a 10% rise in the detection of illegal immigrants, but Mr Clark must “take full responsibility for his actions”.
Mrs May has announced there will be three inquiries, the main one led by the Chief Inspector of the UK Border Agency, John Vine.
Shadow home secretary Yvette Cooper said the “fiasco” for the home secretary was getting worse, now her version of events has been contradicted by “her most senior official” at the UK Border Force.
“First she decided to reduce border checks then lost control of her so-called ‘pilot’. Now she has lost the loyalty of one of her most senior civil servants. The home secretary clearly doesn’t know what has been happening at our borders.”
Labour MP Keith Vaz, the chairman of the home affairs committee, said Mr Clark “cast very serious doubt” on the home secretary’s account his committee had heard just hours earlier.
“It’s completely contradictory to what she said. This is a complete turnaround of events.”
Chief executive of the UK Borders Agency Rob Whiteman said he suspended Mr Clark after he 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 went further than was approved,” he added.