It is the latest health scare to erupt in France, coming after controversies involving later-generation contraceptive pills, breast implants and a pill used as a dietary aid that was linked to heart failure.
The National Agency for the Safety of Drugs and Health Products (ANSM) said it was suspending sales of a hormonal treatment called Diane 35 made by German firm Bayer.
The move will be phased in over three months to allow users to find an alternative drug, Dominique Maraninchi, the agency's director, told a press conference.
The product is authorised for treating acne in young women, but doctors have been prescribing it as a contraceptive because it stops ovulation, he said.
"This drug is not licensed for use as a contraceptive," Maraninchi said. "But it is being used as such, in this secondary role ... yet there are plenty of other alternative contraceptives that can be used in this country."
Blood clots attributed to Diane 35
Over 25 years, four women have died from blood clots attributed to Diane 35, according to ANSM, which said more than 300 000 women in France are using it as a contraceptive.
Bayer, in a statement to Agence France-Presse on Sunday, said the risk of clots "is a known effect, and is clearly marked as such in the package advice for patients."
It added that Diane 35 should only be prescribed for acne, and "in the context of a medical consultation, with respect for appropriate use, side effects and precaution."
France has been shaken by a series of health scares in recent years.
It has asked the European Medicines Agency to change prescription guidelines for so-called third and fourth-generation oral contraceptives after these drugs were found to carry a higher risk of blood clots compared to earlier versions.
In 2010, the French authorities called down breast implant manufacturer Poly Implant Prothese after it was found to be using non-authorised silicone gel that caused a high rate of implant ruptures. Health experts disagree on the risks though.
Another scandal concerns an anti-diabetes drug called Mediator, manufactured by the French pharmaceutical company Servier, which was being used as a slimming aid because it reduces hunger pangs.
The drug was pulled off the market in 2009 after evidence emerged of hundreds of deaths caused by damage to heart valves.
Diane 35 is sold in 116 countries around the world, according to the ANSM website. – AFP