The county has a rate of 257.6 per 100,000 with 410 new cases, from the period of September 19th to midnight October 2nd.
Monaghan has the second highest rate with 189.0, followed by Dublin with 172.8 and Roscommon with a rate of 142.5.
Overall, there has been a total of 5,142 confirmed cases of Covid-19 from September 19th to October 2nd.
The current national incidence rate has risen slightly to 107.98 during that same period.
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The number of cases over the past 14 days associated with clusters was 2,417, which is close to half of all cases.
Community transmission meanwhile accounted for 1,283 cases during the period.
This comes as the number of people currently being treated with Covid-19 in hospital has increased to 134.
That is up from yesterday's figure of 113, according to the HSE, while 22 people are being treated in intensive care.
Yesterday, the acting chief medical officer warned of a "serious escalation" in the coronavirus trends.
613 new cases were recorded yesterday, the highest daily figure since mid April, with 726 new infections in the North - the second highest recorded there since the start of the pandemic.
Public health expert Dr Gabriel Scally says having different approaches to tackling the virus on both sides of the border is not working:
"I think it is a failure of our politicians to really grasp this fantastic opportunity to have an all island approach.
"If it was a disease in cattle or pigs, we would have been absolutely on top of this. There would be no question of doing things differently from Strabane to Lifford, but is absolute nonsense!"
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