Some 222 cases were recorded by the Department of Health on Saturday, and a further 176 cases on Sunday.
This brings the total number of cases in the region to 9,341, including 977 positive results confirmed in the last seven days.
Updates on the number of deaths will come on Monday.
Stormont Health Minister Robin Swann described the figures as “deeply concerning”.
“Important decisions to be taken in the days and weeks ahead. Everyone must play their part by following public health advice,” he tweeted.
Latest figures of Covid-19 cases deeply concerning.
Important decisions to be taken in the days & weeks ahead.
Everyone must play their part by following public health advice.
✅ Keep your distance
✅ Wash your hands
✅ Wear a face covering
✅ Download the StopCovid NI App https://t.co/0oVnUaHhfDAdvertisement— Robin Swann : North Antrim UUP MLA (@RobinSwannMoH) September 20, 2020
Deputy First Minister Michelle O’Neill highlighted an increase in Covid-19 cases across Ireland and warned against denial and complacency.
“There have been over 3,000 new Covid-19 cases and 17 Covid-19 deaths on island of Ireland this week,” she tweeted.
“The virus is spreading rapidly within communities and claiming lives – this is the reality Covid-19 denial and complacency will result in more deaths. We must work together to save lives.”
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Earlier the chairman of the Stormont health committee has referred to “areas of grave concern” within the Covid-19 testing system in Northern Ireland.
Colm Gildernew said his committee wants to speak to Mr Swann about rising case numbers and issues in the testing system.
The Sinn Fein man has also urged that answers are provided to the families of five patients who died at two hospitals in the region, with coronavirus, in the last week.
“The families are entitled to know the truth of what has happened in their loved one’s case, but also the health service needs to very quickly learn how this happened and how they can prevent it happening in further settings,” he told the BBC.
Three of the deaths were at Craigavon Hospital and two at Daisy Hill Hospital in Newry.
The Southern Trust said a level three serious adverse incident (SAI) investigation will be carried out into the outbreak at Daisy Hill. An SAI into the outbreak at Craigavon Area Hospital is already under way.
Meanwhile, Mr Gildernew outlined some examples of problems within the testing system, including a family who are self-isolating after their child was tested on Thursday and are still waiting for a result.
“They have been told at times over the phone to speak to people in England, then Scotland, and when they actually got to speak to somebody here they were told that the test hadn’t been found, so those are areas of grave concern and I think they need to be addressed urgently by the minister,” he said.
