The under-fire UK Border Agency (UKBA) is "nothing like good enough" in certain areas, Immigration Minister Damian Green declared today.
Taking questions from MPs over the border controls row, the Tory minister said the agency was a "mixed bag" in need of improvements.
The top civil servant at the Home Office, of which the UKBA is part, also raised concerns about "cultural issues" in the leadership of the border force.
Permanent secretary Dame Helen Ghosh said the recent controversy had highlighted problems with how information was relayed back to the Home Office and ministers.
Mr Green and Dame Helen appeared before the Commons Home Affairs Select Committee over the relaxation of border controls for non-EU nationals.
The Immigration Minister insisted there was no way that guidance from 2007 could have justified such a move, as claimed by ex-border force chief Brodie Clark.
He said the 2007 guidance - of which neither he, Home Secretary Theresa May or Dame Helen were aware - only permitted relaxed controls for European passport holders.
It was "absolutely wrong in principle" to suggest that officials could "stretch" the guidance to cover the suspension of fingerprint checks because these were only ever required of non-EU nationals who needed a visa.
"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 to stop taking fingerprints of people who require visas to come into this country," he said.
Mr Green said he and Mrs May had in July approved a pilot to relax controls on some EU nationals in limited circumstances and nothing else.
The suspension of other controls was never mentioned to him by Mr Clark despite nine meetings between the two men, he said.
"Very relevant information was withheld from ministers and it appears to have been happening for a period of time," Mr Green said.
The minister added that better communication, including six-hourly updates to the UKBA chief executive Rob Whiteman, was part of an "improvement programme" that was "obviously needed".
"The UK Border Agency is now a mixed bag. It's a curate's egg. It's good in parts but it's nothing like good enough in other parts," he told the committee.
"What we need now is to get more information and have that information spread around so that we can take decisions earlier and we can take decisions faster. That's very much Rob Whiteman's vision, which I share."
Dame Helen said that Mr Clark, who was suspended and later resigned, had failed to mention the suspension of controls in any of his weekly updates from the border force.
"None of them mentioned this issue," she said.
Asked whether he had been given an instruction not to exceed the authority given under the pilot scheme, she said: "Yes. There was an explicit email instruction from the Home Secretary to Mr Clark to that effect."
Dame Helen said: "Of course recent events give us pause about how in any complex organisation like this we understand what is happening at the front line."
She added: "It gives us cause to consider the chain of management information and our process for checking it.
"I think it also raises cultural issues about the leadership at the border force. Also, ministers were relying on weekly updates from Brodie Clark which never mentioned the issue."
She said there was now a "much more rigorous system" of reporting to the UKBA chief executive.
Asked whether Mr Clark had been a rogue officer, she went on: "I believe that Brodie Clark had a long career in a number of high profile, high risk jobs and he always led from the front."
She declined to describe Mr Clark's career as "distinguished" when suggested by one MP.