The Royal Navy's flagship, HMS Queen Elizabeth, is managing a Covid outbreak after more than 100 crew were infected during a port call in Cyprus earlier this month, officials said Wednesday.

The first cases were identified on or around July 4 when the state-of-the-art aircraft carrier was docked at Limassol port on the island's south coast.

Britain's largest warship docked in Limassol from June 30 until July 5, spearheading the largest UK peacetime deployment in a generation, Carrier Strike Group 21.

"As part of routine testing, a small number of crew from the Carrier Strike Group have tested positive for Covid-19," a Royal Navy spokesperson said.

"All personnel deployed have received both doses of the Covid vaccine, and there are a number of mitigation measures onboard, including masks, social distancing, and a track and trace system.

"The Carrier Strike Group will continue to deliver their operational tasks, and there are no effects on the deployment."

According to UK newspaper The Sun, almost half the warships in the carrier strike group have been hit by positive cases.

The Royal Navy's flagship, HMS Queen Elizabeth, leaves Portsmouth Naval Base on the south coast of England, on May 1
The Royal Navy's flagship, HMS Queen Elizabeth, leaves Portsmouth Naval Base on the south coast of England, on May 1 AFP / Adrian DENNIS

It said they include at least 100 crew of the HMS Queen Elizabeth after sailors "were given a run ashore in Limassol".

During her five-day call at Limassol port, HMS Queen Elizabeth welcomed on board dignitaries including Cypriot President Nicos Anastasiades.

UK defence minister Ben Wallace said the outbreak had prompted no rethink of the carrier group's planned 40-country tour.

There are 3,700 personnel across the entire carrier group, including the 1,600 on the HMS Queen Elizabeth.

Wallace told a press briefing on Tuesday: "Our crew are double vaccinated, so you'll be glad to know there is no serious effects on any of the crew, and we will manage it."

HMS Queen Elizabeth is leading nine United Kingdom Carrier Strike Group (UKCSG) ships on a 26,000-mile deployment across the Mediterranean, the Indian Ocean and East Asia.

Cyprus is suffering a fourth wave of coronavirus driven by the aggressive Delta variant, with infections hitting a record 1,081 on Tuesday.

The Republic of Cyprus has confirmed a total of 86,185 cases and 382 deaths in the pandemic.