Sanofi Pasteur and Daiichi Sankyo on Friday announced a recall of the ActHIB vaccine in Japan after an "unidentified substance" was found in two syringes.
Daiichi is the Japan marketer of the vaccine manufactured by Sanofi Pasteur, a wing of Paris-headquartered Sanofi-Aventis. The drug is used to prevent bacterial infections causing pneumonia and meningitis.
However, Daiichi told AFP most of the 1.3 million dose shipment had already been used and only a small percentage remained.
A Sanofi Pasteur official told AFP the company was checking how many vaccines had been used.
The official in Tokyo said that the doses "were manufactured on a production line dedicated to the Japanese market".
"They were delivered between September 2010 and late January 2011 but were produced about six months earlier," he added.
Japan's health ministry last week suspended the vaccine along with Pfizer's Prevenar, also used against bacteria that can cause meningitis and pneumonia.
The ministry is investigating the recent deaths of six infants who were administered either one or both of the treatments, or in combination with other drugs.
Both Pfizer and Sanofi-Aventis have vouched for the safety of their vaccines and said they are cooperating with the investigation in Japan.