South Korea's prime minister on Tuesday apologised for "failing to carefully take care of the health" of hundreds of sailors who contracted coronavirus on a navy ship taking part in an anti-piracy mission off East Africa.

The outbreak aboard the destroyer Munmu The Great is the largest cluster South Korea's military has seen.

A total of 247 of the ship's 301 crew have tested positive for Covid-19 in recent days and two military planes had to be dispatched to fly them all home.

None of the destroyer's crew had been vaccinated because they left South Korea in early February, before the start of the country's vaccination campaign.

The country's prime minister Kim Boo-kyum said in televised comments that the government is "very sorry for failing to carefully take care of the health of our soldiers who are devoting themselves to the country".

In a separate address, defence minister Suh Wook said he "feels heavy responsibility for (the outbreak) and offers words of sincere apology" to the sailors, their families and the public.

Mr Suh said all of the sailors will be moved to hospitals or quarantine facilities upon their return to South Korea on Tuesday evening.

He said the government will work out measures to prevent similar outbreaks involving South Korean troops dispatched abroad.

The cause of infections at the 4,400-ton-class destroyer has not been announced.

But military authorities earlier suspected the outbreak might have begun when the destroyer docked at a harbour in the region to load goods in late June.

South Korea has been engaging in anti-piracy operations in the Gulf of Aden since 2009.

The military planes dispatched to bring back the sailors were carrying other navy personnel who are to sail the Munmu The Great to South Korea for a journey expected to take one month.

Another South Korean destroyer was on its way to the area to replace the Munmu The Great, according to the Joint Chiefs of Staff.

The outbreak on the destroyer comes as South Korea is battling its worst surge of the pandemic at home.

On Tuesday, South Korea reported 1,278 new virus cases.

It was the 14th day in a row that South Korea has reported more than 1,000 new cases.

Since the pandemic began, South Korea has reported 180,481 infections and 2,059 deaths.