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A causal link between the vaccine and the deaths has not yet been established, according to the ministry and Takeda Pharmaceutical Company, which distributes the Moderna vaccine in Japan.
Japan suspended the use of about 1.63 million doses of the Moderna vaccine on August 26 as a precaution after foreign substances were found in some vials.
While inquiries are being conducted by the Japanese government and three pharmaceutical companies involved, no police investigation has been announced and there is no present indication of wrongdoing.
"Currently, no link has been confirmed between these deaths and the Moderna vaccine, but we believe it is important to carry out a formal probe to investigate the matter further," Takeda Pharmaceutical Company said in a statement released Saturday.
Japan's Ministry of Health will conduct that investigation alongside Takeda, the company stated, adding that Moderna has its own investigation underway.
Rovi, a Spanish company that manufactured the batches, described the contaminant as "particulate matter" in a statement Thursday. Rovi said it is also investigating the contaminated lots.
The 1.63 million doses came from three identified lot numbers -- 3004667, 3004734 and 3004956. The doses had been distributed to 863 vaccination sites across Japan, and some were used.
The health ministry said it began notifying the vaccination sites on Thursday morning about the contamination risk.
The two people who died had received vaccines from lot 3004734, one of the lots removed from circulation Thursday. Japan's Ministry of Health, Labor and Welfare said that no foreign contaminants had been reported from this lot yet.
Results from laboratory tests from contaminated samples will be available in the coming days, according to Takeda.
CNN has reached out to Moderna for comment.