South Australia will change how it handles the ongoing COVID-19 pandemic as it prepares to end the state's emergency management declaration.

The new Labor government has introduced legislation to amend the Public Health Act to allow for some virus restrictions to be carried over after the planned lifting of the emergency declaration by June 30.

The new laws will allow for continued measures such as vaccine and mask mandates in hospitals, aged and disability care, and other healthcare settings.

They will also allow rules to be set for virus-positive people and their close contacts.

But they will not provide for the imposition of lockdowns, hospitality restrictions and broader mask mandates.

Premier Peter Malinauskas said South Australians had been subject to the emergency declaration for more than two years and it was time for it to end.

"When the declaration ends, it is important that we still have some protections in place for our most vulnerable South Australians," he said.

"These South Australians are most at risk from being seriously ill if they contract COVID."

Health Minister Chris Picton said he had briefed opposition and crossbench MPs about the proposed changes and the government hoped to get the legislation passed by the end of May.

But he said it did not signal an end to the pandemic with authorities still managing a significant number of cases in the community.

The state's Emergency Management Council, which currently rules on pandemic measures, will also continue to operate.

"This is by no means over but we're doing what we can to manage it," he said.

The government's move comes after officials on Tuesday confirmed two new coronavirus sub-variants had been detected in SA.

The latest whole-genome sequencing among infections reported last week found one case of the Omicron BA.4 variant and one of the BA.5 variant.

Both were detected in returned international travellers.

Chief Public Health Officer Nicola Spurrier said the number of cases of the new sub-variants was expected to increase and there was some preliminary evidence they were more transmissible.

But she said it was too early to tell what impact they might have on total infections and hospitalisations and too early to look at imposing any new restrictions.

South Australia has few virus restrictions after dropping widespread mask mandates before Easter and last week removing the need for close contacts to isolate.

SA reported 3591 new infections on Wednesday along with 12 more deaths, some of those dating back to April 19.