In a tweet, the ministry said this had resulted in the number of people hospitalised since the start of the pandemic increasing by more than 5000, from 14,043 to 19,476.
The ministry said it was due to a "coding issue".
The ministry said the miscounting had "no impact" on the advice it provided about Covid-19 settings. This was because the daily hospitalisation data, captured by a different system, was used to inform the ministry's advice.
Ardern said she had not been properly briefed on the issue, but assured the numbers did not have any impact on Government decisions being made at the time.
On Covid-19 case numbers, Ardern said modelling had predicted a wave of cases similar to what was being experienced currently.
It was predicted there could be a small increase but much lower than the Omicron wave at the start of the year.
The Government was not currently considering relaxing or increasing restrictions, including the seven-day isolation period, she said.
On current levels of restrictions, the country was still in a period of Covid-19 waves.
The country was in a much better place than a year ago, being highly vaccinated and with anti-viral medication available, she said.
Ardern said she could not say when all current restrictions would be removed.
The Covid-19 Epidemic preparedness notice, which gives the Government the power to implement Covid-19 restrictions and rules - such as mask mandates - is due to expire on October 20 unless it is renewed before then.
Cabinet had considered letting it lapse three months ago when it decided to drop the traffic light system, but opted to renew it then to allow it to continue to require masks in health settings. It is expected to decide today whether to renew it again - which requires the PM to state she is satisfied Covid-19 is "likely to continue to disrupt essential governmental and business activity in New Zealand significantly".
