A pharmacist saw several black particles in one vial of the vaccine in Kanagawa Prefecture, according to authorities.
Some 3,790 people had already received shots from the batch. The rest of the batch has now been put on hold.
It comes less than a week after Japan suspended the use of about 1.63 million Moderna doses due to contamination.
The pharmacist found the black particles while checking for foreign substances before the vaccine's use.
The jab's domestic distributor has collected the vial suspected to be contaminated.