Speaking at Westminster, Minister of State for Defence Baroness Goldie also revealed some military personnel on active operations overseas had refused to be vaccinated.
Responding to questions in Parliament, Baroness Goldie said the proportion of UK Armed Forces currently serving in Estonia confirmed to have COVID-19 was 13.2% on 28 June.
According to the Army, about 900 soldiers are deployed to the Baltic country, which would put the number infected at approximately 118.
UK military personnel have maintained a rotating presence in Estonia since 2017, with troops taking on a leading role in NATO's response to a developing threat from neighbouring Russia.
Operation Cabrit sees about 800 to 950 British service members lead efforts to tighten Euro-Atlantic security alongside French, Danish and Estonian forces.
WATCH: Baroness Goldie details COVID cases for overseas Personnel
Baroness Goldie told peers the higher case rate in Estonia was due to a "significant changeover" in personnel.
Updating the chamber on the vaccination of UK personnel on "active operations", the Conservative frontbencher said that as of 28 June, 95% had received a first dose, 74% had received a second dose – up from 61% last week – while 2% "had refused a dose".
For those based overseas, excluding operations, 73% had received a first dose and 35% a second.
Speaking outside the chamber, Labour frontbencher, Lord Coaker, said: "Given the significant difference in the Estonia figure from other areas of overseas deployment, the Government must give a full explanation of what has happened – including any lessons to be learnt.
"Meanwhile, on the wider issue of those serving overseas who have declined the offer of a vaccine, it would be useful for ministers to say what consequences this has had for their deployment."
Cover image: Troops, as part of NATO's enhanced Forward Presence, training in Estonia earlier this year (Picture: NATO).