The probe was launched after provincial and health authorities reported that since November, about a half-dozen babies died soon after receiving the hepatitis B vaccine made by Biokangtai.
Health authorities suspended the use of Shenzen-based Biokangtai's hepatitis B vaccine on Friday after the first deaths of babies were reported.
Four babies reportedly died in the southern province of Guangdong, although one was said to have died from pneumonia. The National Health and Family Planning Commission reported that two babies in Hunan province and another in Sichuan had died in a similar way.
Autopsies were being conducted and results were expected in a few weeks.
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Hepatitis B is a chronic liver infection that is spread through the blood or bodily fluids of infected people. It can cause liver inflammation and jaundice.
The vaccine was given to children free of charge as part of the government's national immunisation programme.
In a statement earlier this month, Biokangtai said it was confident of the safety of its products and that the deaths could be caused by underlying diseases that coincidentally began showing symptoms after the vaccinations.
China has seen a series of product safety scandals over the past few years. At least six children died in 2008 after drinking milk contaminated with the industrial chemical melamine.
People are suspicious about Chinese health authorities and the country's drug safety standards, though improvements have been made in recent years since government agencies withheld information about the spread of SARS and bird flu in 2003.