The Immigration Service Union told BBC Radio 4’s PM that about half of those trained to work during the strike did not have the relevant security vetting.
An immigration officer said he was 100% sure people had been stamping passports without the necessary clearance.
Immigration Minister Damian Green said all those on duty had been cleared.
“They’re all trained to the level they need to do the job they’ve been doing,” he said. “Everybody has been cleared to the appropriate level for what they’ve been asked to do today.”
Mr Green told PM he would look at the concerns that the Immigration Service Union had raised.
BBC correspondent Jon Manel says he has seen a letter sent to some government departments last week by the head of the Civil Service Sir Gus O’Donnell asking for volunteers to work for the UK Border Agency during the strike.
He says that the letter stated that volunteers needed to have been cleared to at least CTC level (Counter Terrorism level) and ideally to SC level (Security Check level).
Speaking on condition of anonymity, an immigration officer on strike on Wednesday told our correspondent that staff with CTC level clearance would not normally be able to stamp passports.
“I think it’s a manipulation of the normal procedures,” the officer said.
Impact of the strike
The Immigration Service Union said 80% to 90% of its members were striking, with 22 out of 23 workers at Calais port not showing up for work and, as far as they were aware, none of their members working at Heathrow.
Public and Commercial Services (PCS) union members who work for the UK Border Agency also went on strike but airport sources earlier suggested to the BBC that immigration controls had been at two thirds of normal staffing levels – more than the 30-50% predicted previously.
Plane arrivals and take-offs at Britain’s two biggest airports – Heathrow and Gatwick – were said to be largely unaffected with only a few cancellations of in-bound transatlantic flights to Heathrow.
Mr Green said it had broadly been “business as usual”.
He told the BBC some suspected illegal immigrants were identified at Heathrow and sent back and that more than 20 people had been stopped at Calais and Dunkirk trying to get into Britain.
“That’s more than we would normally expect on a Wednesday in November, so I suspect there was some opportunist attempt to get across the border and we’ve stopped it.”
Tens of thousands of people joined rallies around the UK as the 24-hour over public sector strike pensions disrupted schools, hospitals and other services.
Unions object to government plans to make their members pay more and work longer to earn their pensions.
Source BBC © 2011