There are concerns Ireland is heading into a fourth wave of Covid-19.
Professor Philip Nolan told a briefing of the National Public Health Emergency Team (Nphet) that the R number has risen, and is now between 1 and 1.2.
He said the rise was "cause for concern" and pointed out that transmission rates were rising within groups of people who were unvaccinated or half-vaccinated.
Deputy chief medical officer Ronan Glynn told the briefing that Donegal has the highest Covid incidence rate in Ireland and there has a been spike in Waterford with high rates also in Limerick.
Deputy chief medical officer Dr Ronan Glynn told the Nphet briefing: "We have some concerns about Dublin, while the incidence is not the highest in the country, the incidence has taken off there versus the rest of the country and given the population size of Dublin, if that continues it will drive the national picture.
"We are aware of the past number of weeks that Delta was present at a greater proportion in the Dublin area.
"One of the things doctors are telling us at the moment is that this is not like previously, that outbreaks are very easily seeding across community, across settings. Once it gets into a community it is spreading much easier than we have seen previously."
Professor Philip Nolan told the Nphet briefing: "We are in a concerning situation, we are seeing an increase in incidents across most age groups and we are seeing a stabilisation in hospitalisations, we would be concerned there might be an increase in those in the coming weeks.
"We are close to 390 cases a day now. We have to be concerned that we are at the beginning of an increase in incidents driven by the Delta variant, that presents significant dangers to the unvaccinated population and the partially vaccinated population. So it is necessary to reiterate the advice that we have to limit transmission as vaccination proceeds."
Professor Nolan added: "If case numbers increase, albeit more slowly than they would have increased in previous waves of the disease, we are looking at high case counts for a very long period of time.
Addressing the spread of the Delta variant, chief medical officer Dr Tony Holohan said: "We are not going to stop this happening, this variant is sufficient in the way of fitness to become the dominant strain across Europe and that is what going to happen.
"It was a question of when, rather than if, and that we would try to slow it down as much as possible while we give as much protection as possible to people who are vaccinated.
"The evidence is that we have slowed this down somewhat, we would like to have slowed it down further. A couple of weeks back it began to move.
"As we have always done when we believe the evidence is there to support us changing policy, we take that action swiftly and proportionately in relation to the concerns that we have.
"We are going to experience very significant transmission. You will see what is happening in Scotland, they are a number of weeks ahead of us. Northern Ireland is probably two or three weeks ahead of us in terms of their transmission.
"All of that says to us in broad terms, we are not going to stop this, but the measures we have taken now have had an effect in slowing down that transmission."