While latest figures show cases continuing to fall in the one time hotspot of Derry and Strabane, rates in the nearby south Inishowen area – which directly tracks the border – have spiked at almost 600 per 100,000 people.
The entire Donegal county recorded its highest daily rate on Thursday and its main hospital in Letterkenny also confirmed it was dealing with an outbreak.
The Republic’s Health Service Executive (HSE) has put the rise down to “small local outbreaks and cross-border issues”.
It is thought some outbreaks have been traced back to parties in areas close to the Derry border.
Cases have increased despite restrictions being in place in Donegal for longer than any other area in the Republic apart from Dublin.
Action was taken by the government at the end of September following a surge in cases in the north west, with an almost full lockdown also ordered across the state last month.
The news comes as restrictions in the Derry and Strabane area appear to be working.
Latest figures show the infection rate has fallen in the last week from almost 400 per 100,000 people to just over 300.
At one point it was the highest in the UK at over 900.
Dr Tom Black, NI chairman of the British Medical Association, said the efforts made by people were paying off and they should continue to adhere to Department of Health guidelines.
However, he expressed concern at the surge in border areas of Co Donegal.
“There is no doubt that the majority of people on both sides [of the border] have been doing their best and only crossing the border for essential reasons such as work,” he said.“But the border is porous and some people are avoiding the main crossings to travel between the two areas.”
The Derry-based GP said if travel was restricted to necessary journeys, each region would have the power to control the spread of Coronavirus in its own area.
“When we were reporting the highest figures a few weeks back, I appealed to people in Derry and Strabane not to cross the border unless it was vital.
“It’s only fair therefore that I make the same appeal to Donegal people now, not to travel north unless your journey is necessary.”
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