The deaths are reportedly the first ones to happen in the Armed Forces.
The Sun reports that the Ministry of Defence confirmed the Royal Navy sailors were not at sea when they fell ill.
Armed Forces personnel have been helping with the coronavirus response effort across the country.
A Freedom of Information request revealed that two Royal Navy sailors died between March 1 and April 16, they have not been named.
It also showed that 121 service personnel including 58 from the army, 34 from the navy and 29 from the RAF, had fallen ill with Covid-19 during that time frame.
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Two sailors from HMS Queen Elizabeth’s crew tested positive for Covid-19 during the round of testing that took place in April, before she department Portsmouth.
All of its 700-strong crew were tested for the virus and it delayed the departure of the 65,000-tonne aircraft carrier until the start of May.