Picture used for illustrative purposes only.

Two people died after receiving Moderna Inc coronavirus vaccine shots that were among lots later suspended following the discovery of contaminants, Japan's health ministry said on Saturday.

The men in their 30s died this month within days of receiving their second Moderna doses, the ministry said in a release. Each had a shot from one of three manufacturing lots suspended on Thursday. The causes of death are being investigated.

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Japan halted the use of 1.63 million Moderna doses shipped to 863 vaccination centres nationwide, more than a week after the domestic distributor, Takeda Pharmaceutical Co, received reports of contaminants in some vials, according to Reuters.

"At this time, we do not have any evidence that these deaths are caused by the Moderna COVID-19 vaccine," Moderna and Takeda said in a statement on Saturday. "It is important to conduct a formal investigation to determine whether there is any connection."

A health worker prepares to administer a vaccine dose.

The government has also said no safety or efficacy issues had been identified and the suspension of the three Moderna batches was a precaution.

Meanwhile, Tokyo city hall has apologised for "confusion” amid its vaccination rollout targeting young people, after crowds looking to get the shot were turned away from a facility in the Shibuya district.

Health authorities on Saturday switched to a reservation system instead of first come, first served. But more than 2,200 people showed up to get vaccine appointment vouchers, some waiting in line since dawn, and 354 were selected by lottery to receive shots, Japanese media reported.

Inoculations for those ages 16 through 39 began on Friday.

Japan, which has one of the slowest COVID-19 vaccine rollouts in the developed world, has prioritized giving shots to elderly people and then gradually working its way down by age group.

The latest development appears to counter critics who had suggested young people wouldn't be interested in getting vaccinated.