Home Secretary Theresa May has admitted she relaxed border controls at all UK ports during the peak summer period.
But senior officials at the UK's border force went even further, scrapping key checks against a Home Office database without ministerial approval.
The number of suspected terrorists, criminals and illegal immigrants who entered the country as a result of the move will never be known, Mrs May said.
Three staff, including the head of the UK border force Brodie Clark, have been suspended and those responsible will be punished "to make sure that border force officials can never take such risks with border security again", she said.
"As a result of these unauthorised actions, we will never know how many people entered the country who should have been prevented from doing so after being flagged by the warnings index."
Mr Clark confirmed he had gone further than the pilot scheme allowed when John Vine, the independent chief inspector of the UK Border Agency (UKBA), raised concerns last week, she said.
Biometric checks on European nationals and checks against the Home Office database on children from the European Economic Area (EEA) "were abandoned on a regular basis, without ministerial approval", Mrs May said.
Adults were not checked against the database at Calais and the fingerprints of non-European nationals from countries that require a visa were stopped, all without ministerial approval, she said.
"I did not give my consent or authorisation for any of these decisions," Mrs May told MPs.
"Indeed I told officials explicitly that the pilot was to go no further than we had agreed."
