A small numbers of the BCG formula did not meet end-of-shelf-life specifications, Powderject Pharmaceuticals Plc said.
The Department of Health welcomed the "prudent and responsible" course of action the company had taken and a spokesman said no concerns about the safety of the vaccine had been raised.
Powderject was awarded a £32m government contract to supply smallpox vaccine to protect 20 million Britons in the event of a germ warfare attack by terrorists.
Secret deal
The deal, which was done without public competition, was widely criticised in April because the head of the company, chief executive Paul Drayson, was a Labour Party donor.
And the company came under scrutiny again when a US report cast doubt on whether the UK had bought the right type of smallpox vaccine.
The problem with the BCG vaccine was initially identified in Ireland when a "small number" of batches approaching the end of their normal three-year shelf life were found to be "potentially less potent than normal".
Further testing identified a similar problem in a number of other batches at which point it was decided to order the recall.
School vaccine
The company said it had consulted independent experts who had confirmed that the vaccine should still be effective but it was being "extra cautious".
The Department of Health spokesman said the school vaccination programme would not be affected because it was not due to restart until October.
Sole supplier
"At this stage there is no need to recall people for re-vaccination but the situation is being kept under review," he added.
Currently no other BCG vaccine is licensed for use in the UK.
The government was forced to defend its links to the company, including the supply of BCG, when the smallpox deal was revealed.
Health minister Yvette Cooper said at the time: "Powderject was the only manufacturer with a UK licence to supply the BCG vaccine at that time."