Stephen Donnelly and Ireland’s chief medical officer held a virtual meeting with local politicians over the weekend.
The rate of infection in the county is currently almost 300 cases per 100,000 people, compared to 127 nationally.
The rate has been almost continually above the country’s average since last September.
Across the border, Department of Health announced on Thursday that there had been a further 28 positive cases in the Derry City and Strabane District Council area in the past 24 hours, a rise of four on the previous day.
Within the past week there have been a further 121 COVID-19 cases in the Derry and Strabane area.
That means that since the pandemic started in March there have now been 12,227 positive cases within the council boundary – the fourth highest among all 11 councils in the North.
The rate of infection within the Derry and Strabane council area is now up to 80.3 cases per 100,000, the highest in the North of Ireland.
The Department has recorded a total of 136 coronavirus deaths within the Derry and Strabane council area to date – the third lowest out of all councils here.
The Department’s most up to date figures will not be released until tomorrow, Tuesday, May 4 because of the May Day public holiday. It has also announced that it will no longer publish data over the weekend from now on.
Mr Donelly said the weelend meeting was “very supportive”.
In a tweet, he said: “A lot of good work already happening that can be supported. Thanks to all involved.”
Speaking after the meeting, Donegal TD Charlie McConalogue said there was a clear desire in the community to bring down the infection rate, RTÉ reported.
Attendees spoke of the need for more walk-in test centres outside of Letterkenny, as well as better public health messaging via local media, according to RTÉ.
Independent TD Thomas Pringle said the high rates along the border were disappointing, but unsurprising due to the Irish government’s “mixed messaging”.
Earlier on Saturday, Mr Donnelly said health chiefs would consider sending “additional supports” to the county.
He added: “Spikes like this occur in many counties.
“Huge local efforts have been made and the community will continue these efforts.”
On Friday, Dr Tony Holohan warned of the county’s persistently high infection rates.
Speaking at a department of health briefing, he said there were “clear examples of non-compliance across many parts of society. It is a concerning level of compliance compared to the rest of the country.”
Meanwhile, the North of Ireland’s Public Health Agency (PHA) has made a joint appeal with the southern Health Service Executive, warning rates could rise “significantly” on both sides of the border if people are not vigilant.
Dr Gerry Waldron, from the PHA, said: “We know there is a temptation to travel either side of the border to engage in activities as lockdowns ease.
“But if we see large numbers gathering or people abandoning public health advice, we could see cases rise significantly on both sides of the border.
“Viruses don’t recognise borders, so we all need to act with caution.”
The warnings come after the Irish government announced a phased relaxation of its strict Covid-19 lockdown over the next six weeks.
The country has been at Level Five, its highest level of restrictions, since Christmas.
On Saturday, the Republic recorded three more Covid-19-related deaths, bringing the country’s total number of deaths to 4,906.
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