The number of its staff testing positive or being forced to self isolate because of contact with colleagues with the virus is understood to have increased in the past week.
Six services on the line were affected from Saturday with a number of trains between Ayr, Girvan and Stranraer no longer running from Monday to Saturday.
The 0653 Girvan-Kilmarnock and 1903 Stranraer-Kilmarnock services will now start at Ayr, while the 1809 Glasgow-Stranraer and 2108 Kilmarnock-Girvan services will terminate at Ayr.
In addition the 0612 Ayr-Girvan and 2203 Girvan-Ayr service services have been withdrawn.
This comes on the back of a series of timetable reductions and changes in the south west in December due to falling passenger numbers.
The operator said passenger numbers nationally have reduced from 15 per cent to 10 per cent of normal across its network following the start of the latest lockdown.
They had fallen as low as five per cent at the start of the pandemic crisis last March.
The number of ScotRail trains running has already been reduced to 81 per cent of normal but more reductions are planned.
South Scotland list MSP Colin Smyth, who is also Scottish Labour’s Transport spokesperson, Colin Smyth said: “While the situation we are currently living through is completely unprecedented, the reduction of these vital services is still a blow to rail travel in the south west of Scotland.
“I recognise that considerably fewer people have been travelling for months due to Covid-19 travel advice urging them against non-essential travel on public transport, but there is a real fear that when the situation starts to improve, and more people start using our railways again, that these services won’t be reinstated.
“The recent increase in Covid-19 cases in the Stranraer area remains a huge concern and this has had a direct impact on staff availability on these train services.
“I would urge everyone to continue to adhere strictly to the rules and stay at home as much as possible.”