The pause came into effect on Thursday, more than a week after reports of contaminated vials.
Both Japan and Moderna said that no safety or efficacy issues had been identified and that the suspension was just a precaution.
But the move prompted several Japanese companies to cancel worker vaccinations planned for Thursday.
The vaccine has recently been approved for 12 to 17-year-olds in the UK.
“Moderna confirms having been notified of cases of particulate matter being seen in drug product vials of its Covid-19 vaccine,” Moderna said in a statement.
“The company is investigating the reports and remains committed to working expeditiously with its partner, Takeda, and regulators to address this,” it added, referring to Japan’s Takeda Pharmaceutical, which distributes the vaccine in the country.
Takeda first found out about the contaminated vials on August 16 and reported the issue to the government on Wednesday, a health ministry official said.
The delay was because the company needed time to gather information on which vials were affected and where they were in the country, the official added.
Moderna said the contamination could be due to a manufacturing issue in one of the production lines at its contract manufacturing site in Spain.
Spanish pharma company Rovi, which bottles or “fills and finishes” Moderna vaccines for markets other than the United States, said it is investigating possible contamination of Moderna doses and the issue appeared to be limited to a few batches bound for Japan.
The suspension is a fresh setback for Moderna, whose partners had production delays last month that disrupted supplies to countries, including South Korea.
Moderna and Takeda did not immediately reply to Reuters’ requests for comment.
Japan’s defence ministry, which operates a mass vaccination site in Osaka, said shots from the lot in question, which contains 565,400 doses, had been used in the western prefecture between August 6 and August 20, but it did not say how many people were affected.
Moderna said that “out of an abundance of caution” it had put the lot in question and two adjacent lots on hold.
Takeda said it conducted an emergency examination after particulate matter was found in a lot of vaccine vials at an inoculation site.
Prime Minister Yoshihide Suga said the country’s inoculation plan would be little affected by the issue.
A day earlier, he said about 60 per cent of the public will be fully vaccinated by the end of September and the country had enough vaccines to provide booster doses if such a decision is taken.
Chief Cabinet Secretary Katsunobu Kato said there had been no cases reported of health issues related to contaminated shots administrated.