One of them is Cork, where a fifth of cases in the past two weeks have been linked to pubs and restaurants.
While in Galway, there's been a large cluster following a house party attended by young people.
390 new cases of Covid 19 were confirmed last night and no further deaths.
Acting chief medical officer Dr Ronan Glynn says there are some areas he will be keeping a close eye on.
He said: "Unfortunately we're seeing particularly fast increasing incidence [of Covid-19 infection] in a number of counties. I want to highlight Cork and Galway, which we've been doing now for about a week, but also Monaghan and Roscommon, because their overall population sizes are lower, their incidences can rise very quickly with a relatively small number of cases but that said, they do stand out for the speed of which the situation there is deteriorating."
There were no new Covid-19 related deaths and 390 additional cases confirmed by the Department of Health yesterday.
Of the additional cases, two thirds were under the age of 45. 36 per cent are confirmed to be associated with outbreaks or are close contacts of a confirmed case, while 45 cases have been identified as community transmission.
209 of yesterday's cases were located in Dublin, 27 in Cork, 22 in Donegal, 21 in Galway, 14 in Kildare, 14 in Monaghan, seven in Roscommon, seven in Tipperary, seven in Waterford, seven in Wexford, six in Limerick, six in Longford, five in Laois, five in Meath, five in Offaly, five in Sligo, with the remaining 23 cases spread across eight other counties.
Cork and Galway
Dr Glynn highlighted Cork and Galway as regions of concern but added the purpose of highlighting these areas was not to say they would enter a lockdown, but rather to say to people living there that this is "still in your control" and additional measures could be avoided.
He said that Limerick, Waterford and Tipperary were examples of places that had done "really well," that had "turned around situations that were going in the wrong direction".
The Restaurants Association of Ireland has accused the acting chief medical officer of 'tarnishing' the industry with one 'sweeping statement'.
The RAI's chief executive is calling for more information about where cases linked to restaurants in Cork have arisen.
Adrian Cummins says the whole sector shouldn't be blamed for this.
Mr Cummins said: "It warrants further exact information from the comments made by the chief medical officer. You cannot tarnish an entire industry with a broad sweeping statement like that."