The head of the UK border force has been suspended by the Home Office following claims some passport checks were not carried out during the summer.
Brodie Clark also sits on the board of the UK Border Agency, of which the border force is part. Two other UKBA officials have also been suspended.
It is alleged staff were told to relax identity checks on non-EU nationals.
The Home Office is investigating. In July it said EU national checks could be reduced in "limited circumstances".
Senior UKBA official Graeme Kyle, who is director of operations at Heathrow Airport, is one of the two others suspended.
Staff working for the UK border force are responsible for checking passports and conducting immigration raids.
In a statement, the Home Office said ministers had agreed in July that EU nationals could have their biometric passport checked "upon the discretion of a UKBA official" instead of automatically.
In addition, European school children travelling with their families or in groups would not automatically be checked against watch-lists - known as the warnings index - aimed at flagging up those who may be "of interest" to the border agency.
The Home Office statement added: "Instead, Brodie Clark is alleged to have authorised UKBA officials to abandon biometric checks on non-EEA (European Economic Area) nationals, the verification of the fingerprints of non-EEA nationals and warnings index checks on adults at Calais."
BBC home affairs correspondent Tom Symonds said the mention of Calais referred only to the warnings index checks. The other checks were allegedly abandoned elsewhere.
He said the Home Office did not know the precise extent to which checks were relaxed.
Biometric passports contain a digital image of the holder's face which can be used to compare with the printed version and check the passport has not been forged.
Home Secretary Theresa May's reaction to the developments was "incredulity and fury", a source told our correspondent.
Mr Clark was at first offered the opportunity of retiring by the UK Border Agency, but, following the intervention of the Home Office, was suspended pending an investigation.
Two investigations have been ordered.
Dave Wood, who heads the enforcement and crime group at the UKBA, will carry out a two-week inquiry designed to discover to what extent checks were scaled down and what the security implications might have been.
Ex-MI6 official Mike Anderson, director general of the strategy, immigration and international group at the Home Office, will investigate wider issues relating to the performance of UKBA.
Our correspondent said one Home Office source had labelled the border agency a "massive problem".
Sue Smith, of the Public and Commercial Services (PCS) Union, said job cuts had led to staffing shortages which forced rules to be relaxed in a bid to "give the travelling public what they wanted".
"The travelling public, understandably, want to have a fast and efficient service, and yet we are also under a reduced work force," she said.
Shadow home secretary Yvette Cooper accused the government of making borders less secure, and said it needed "to get a grip of illegal immigration and border security fast".
The home secretary "needs to answer whether the cuts to 5,000 staff from the borders agency is increasing pressure on officials to cut corners on border security and illegal immigration", Ms Cooper said.
Labour MP Keith Vaz, who chairs the Commons Home Affairs Select Committee, said the allegations were "extraordinary" because they involved such senior members of UKBA.
On Friday, the Home Affairs Select Committee reported that 124,000 deportation cases had been shelved by UKBA.
The cases had been "dumped" in a "controlled archive", a term used by UKBA to try to hide the fact that it was a list of lost applicants, the MPs said.
Ministers and the opposition blamed each other for the reported failings.
Mr Vaz said: "Only a day after the publication of our report, which concluded that the Border Agency continues to fail, we have this remarkable news.
"We will question the home secretary about this on Tuesday when she comes before the committee. If her answers do not satisfy us, I am sure the committee will want to conduct its own inquiry.
"The border police are supposed to keep people out, not let people in."