First Sea Lord Admiral Tony Radakin is self-isolating for 10 days alongside defence secretary, Ben Wallace and five other senior commanders – including the heads, RAF and Strategic Command – after being contacted by NHS Track and Trace.
It comes after the head of the UK’s armed forces, General Sir Nick Carter tested positive for coronavirus.
Adm Radakin had come into contact with Gen Carter on Thursday during a meeting at Defence Academy at Shrivenham, Oxfordshire.
Others in attendance and now forced into isolation included Mr Wallace, General Sir Mark Carleton-Smith, who is head of the army and Admiral Sir Tim Fraser, vice-chairman of the defence staff, Air Chief Marshal Sir Mike Wigston – formerly of Rowner, near Gosport – and General Sir Patrick Sanders, who is commander of Strategic Command.
Gen Carleton-Smith and Gen Carter's deputy spent the weekend in quarantine while they await the result of PCR tests after attending the meeting.
Gen Carter reportedly tested positive on Friday after appearing at the Chalke Valley History Festival.
Social distancing measures were said to have been maintained during Thursday's meeting.
A Ministry of Defence statement said: ‘The Chief of the Defence Staff has tested positive during routine Covid-19 checks. Colleagues who were in a senior meeting with him last week, including the Secretary of State, are self-isolating in line with government guidelines.’
Military business is now being between senior commanders is now being conducted remotely.