NPHET says the spread of Covid-19 continues to be particularly high in Cavan and Monaghan.
Monaghan has the highest seven and fourteen day incidence rates, 2.8 times higher than the national average.
Cavan has the second highest fourteen day rate, and the third highest seven day rate - just behind Donegal.
The country is said to be facing a "long, slow" wave of Covid-19 that won't peak until next month.
Professor Philip Nolan, chair of NPHET's modelling advisory group said the worst affected areas are in the border region.