The department said it was "extremely unlikely" that anyone would contract the disease after it emerged that 40,000 incorrectly labelled doses of the vaccine were sent to family doctors.
A letter has now been sent to GPs advising them to dump the affected supplies and re-vaccinate patients.
A Department of Health spokeswoman said: "Diphtheria is extremely uncommon, and all children have been vaccinated against it in Britain for many years.
"We have sent out a letter asking for the recall of the affected vaccine.
"This is a precautionary measure on the part of the Department of Health and it is very unlikely anyone will contract diphtheria."
The affected vaccine was sent to GPs in 1995, and was stamped "use by 12 February 1999". The use-by date should have been 12 February 1998. The letter highlighting the mistake was sent out in June.
The Department of Health spokeswoman said the blunder happened because the manufacturer of the drug, the Swiss Serum and Vaccine Institute in Berne, recommended that it had a four-year shelf life, while the British health advice was that it should be kept for only three years.
The 1995 vaccine batch was sent out with the Swiss rather than the British use-by date on it, she said.
"Our medical people say if it is kept longer than three years you will have a `sub-optimal' level of cover, but you will still be covered to the level advised by the drug's manufacturers," she said.
Diphtheria is an acute infectious disease of the respiratory tract which is spread through sneezing and coughing.
The disease killed 2,500 people a year in pre-war Britain, but it has been all but eradicated since the introduction of mass childhood inoculation in 1940.
Low-dose diphtheria vaccine is given to travellers as a precaution before visiting certain countries, mostly in Africa and Asia.Reuse content