The ex-border force chief never mentioned the relaxation of checks on non-Europeans to Immigration Minister Damian Green or the Home Office's top civil servant, MPs have been told.
Mr Green said he met Brodie Clark nine times during an approved pilot scheme, but was never told that border staff were routinely going beyond its remit.
Dame Helen Ghosh said he also never mentioned it in his written reports.
Mr Clark has insisted he did not ignore government policy.
Mr Green and Dame Helen both appeared before the home affairs committee which is investigating claims that checks on arrivals to the UK were eased further than was agreed by Home Secretary Theresa May during the pilot.
Mrs May has said she authorised the relaxation of some checks on children from the European Economic Area (EEA), and some extra checks on EEA adults under "limited circumstances", at peak times.
But she claims Mr Clark allowed officials to go further, relaxing fingerprint checks on non-EEA nationals without ministerial approval.
Mr Clark was suspended following the allegations and later resigned, saying his position had been made untenable by Mrs May's statements.
'Wrong in principle'
Last week, Mr Clark told the committee he believed the decision by staff at Heathrow to relax fingerprint checks at particularly busy times was a sensible one and he did not stop it.
He admitted he did not inform ministers about it, despite knowing the home secretary had rejected the possibility of relaxing those same checks as part of the pilot scheme.
He said he believed ministers would have been told about "practices and activities" at the border during "critical" times, arguing that guidelines written in 2007 did allow for some relaxation on health and safety grounds when airports became dangerously crowded.
However, the guidelines do not mention fingerprint checks and do not allow the dropping of any checks on non-EEA nationals.
Mr Green told the committee it was "absolutely wrong in principle" to say that the guidelines could be "stretched" to justify what happened.
"Even if you were using the 2007 guidance as a routine tool of management - which you shouldn't be, it's meant for emergencies - that wouldn't permit you under any circumstances to stop taking the fingerprints of people requiring visas to enter this country."
He added: "It seems to me one of the central confusions of this debate that somehow the 2007 guidelines can cover what was not happening, because they just can't."
Mr Green said he had made regular visits to UK ports and airports, but at no point had been told that the practice was going on.
"Clearly what seems to have happened was that very, very relevant information was withheld from ministers.
"During the period of the pilot I met Brodie Clark nine times so he had ample opportunity to tell me: 'By the way we're not taking secure ID [fingerprints] as well' and he didn't do so."
The minister said he could "only assume... that the people actually on the front line didn't know that what they were doing, or weren't doing, was somehow without ministerial responsibility".
The committee also heard last week from Rob Whiteman, the chief executive of the UK Border Agency - of which the border force is a part, whose decision it was to suspend Mr Clark.
Mr Whiteman said the possibility of Mr Clark retiring rather than facing an internal investigation had been raised.
But he said Home Office permanent secretary Dame Helen Ghosh had intervened and ruled that retirement with a pay-off would not be appropriate given there was a potential disciplinary matter involved.
Dame Helen was asked about the retirement discussion by MPs, telling them that she had objected to the idea of Mr Clark being given "enhanced retirement" package.
This was because she thought it "was wrong" given that he had been suspended on the basis of claims that could amount to gross misconduct.
She said had no power to stop Mr Clark retiring with standard provisions, she said, adding that there had been no pressure from Home Secretary Theresa May.
Dame Helen also said it was "disingenuous" for Mr Clark to say his actions were covered by the 2007 guidelines - and insisted he had never informed ministers about the abandonment of some fingerprint checks.
"In this instance, despite the fact that ministers had requested weekly reports, none of them mentioned this issue about secure ID for non-EEA visa nationals," she said.
Mr Green gave figures to the committee that suggested the pilot scheme was a success - despite it having been suspended following the recent allegations.
He said that in August and September 2010, before it was introduced, there were 737 and 661 "clandestines" apprehended at the borders, while in the same months in 2011, under the pilot, the figures were 809 and 721.
In terms of the number of forged documents identified, Mr Green said 128 and 121 were found in August and September 2010, compared with 135 and 179 in the same months a year later.