Production problems have hit stocks of Depo-Provera, according to manufacturers Pharmacia.
Depo-Provera is used by 330,000 women in the UK. It is a popular long-term contraceptive. A single injection of the drug lasts for three months.
Pharmacia said it hoped supplies would be back to normal by the second week of December.
In a statement, it apologised for any inconvenience caused to doctors and patients.
Production problems
Supplies were interrupted following unforeseen problems during the upgrading of production facilities in Belgium.
The company added that it is working the Department of Health to minimise the number of unwanted pregnancies caused by the interruption to supplies.
Doctors have warned that the interruption to supplies could lead to some women having unwanted pregnancies.
Dr Paul Thornton, a GP in Kingsbury in North Warwickshire, criticised the company saying it should have foreseen the problems.
"They must have seen this problem coming some time ago," he said.
"I have very real worries that this could precipitate a number of unwanted pregnancies."
The Family Planning Association said the interruption to supplies would give GPs and women an opportunity to review their contraception.
"It is a real nuisance but there are alternatives that can be used in the short term," a spokeswoman told BBC Radio 4's You and Yours programme.
"It is a good time [for GPs] to talk to women who don't know about newer long-term progestin methods."
She added: "There are other choices. It isn't a question of suggesting to women that there is nothing else."