The health ministry has decided to suspend the use of two types of publicly subsidized vaccines following the deaths of four children.
Municipal governments were notified of the decision.
The two types are the Hib vaccine, which prevents bacterial meningitis, and a vaccine against streptococcus pneumonia.
There have been no reports so far from the doctors who treated the children that there is a causal relationship between the vaccines and the deaths, according to the Health, Labor and Welfare Ministry.
The ministry is planning to assemble a panel of experts this week after consulting with other doctors to examine the cases, according to officials.
The ministry is expected to let the vaccinations resume if the panel decides the two vaccines don't pose serious safety concerns.
The four children were a 3-month-old girl in Kawasaki who died Feb. 20, a 2-year-old boy in Takarazuka, Hyogo Prefecture, who died Tuesday, a 1-year-old girl in Nishinomiya, also in Hyogo, who died Wednesday, and a 6-month-old girl in the city of Kyoto who died Friday.
The doctors of the children described the causal relationship between the vaccines and their deaths as either unclear or impossible to evaluate. Some had underlying illnesses and others did not.
All four children were administered a vaccine against streptococcus pneumonia made by Pfizer Inc., and all except the girl in Nishinomiya received ActHIB, an Hib vaccine made by Sanofi Pasteur Inc.
In addition, all except the boy in Takarazuka received a mixed vaccine against diphtheria, whooping cough and tetanus on the same day they received other vaccines.
The streptococcus pneumonia vaccine has been administered to an estimated 1.10 million people in 2.15 million doses since it went on sale in February 2010. The Hib vaccine has been administered to an estimated 1.55 million people in 3.08 million doses since its launch in December 2008.
Japan, known for being notoriously slow to accept new vaccines, approved the Hib vaccine in 2007, 20 years after the United States did so. Approval for the streptococcus pneumonia vaccine came in 2009, compared with 2000 in the U.S.
An increasing number of people are believed to be receiving these vaccines because of a subsidy program launched last November in which the government agrees to shoulder half the cost of vaccination if municipal governments organize and subsidize vaccination programs.