The infants died shortly after receiving the vaccines and while it was unclear if there was link between the deaths and vaccines, use of Pfizer's Prevenar and Sanofi's ActHIB will be suspended while the deaths are investigated, the ministry said in a statement.
A ministry safety panel is scheduled to discuss findings in the investigations on Tuesday.
In February last year health authorities in the Netherlands said no relation was found between Prevenar and the deaths of three infants who had received the vaccine.
Three of the children that died in Japan were administered Prevenar together with ActHIB. In addition, three of the children also received a mixed vaccine against diphtheria, whooping cough and tetanus on the same day they received the other vaccines.
Three of the four children died a day after being immunized. The deaths happened between March 2 and March 4.
Representatives for Pfizer and Sanofi in Tokyo said the companies were cooperating with the investigation.
A spokesman for Sanofi said that the company has shipped more than 3 million doses of ActHIB in Japan since 2008 while a spokesman for Pfizer said the firm has distributed more than 2 million doses of Prevenar in Japan since last year.