The quarantine requirement for travellers will now only apply to 20 local government areas in Adelaide and surrounding suburbs.

Health Minister Natasha Fyles has defended the initial call to close the border to the entire state after news emerged at the weekend of a growing cluster in Adelaide's north.

"We didn't know at that point where people might have travelled, where this virus might have spread to," Ms Fyles told reporters on Wednesday.

"So based on that early information we went hard, we went wide but we now are able to reduce the hotspot declaration."

Ms Fyles said health officials in Alice Springs had been overwhelmed with people coming across the border who had been caught out by the change.

The main quarantine centre in Alice Springs was filled to capacity with plans to transfer some people to Darwin thwarted when a plane suffered a bird strike, forcing the flight to be cancelled.

The minister said some local hotels stepped up at short notice to provide rooms and officials were confident clinical safety had been maintained.

But she said it was highly disappointing that other hotels had reneged on taking in quarantine passengers when approached by health staff.

"My understanding is they didn't want to give them over," she said.

"We are disappointed. Fighting coronavirus is a whole of community effort. The efforts that individuals have undertaken, that families have undertaken, have allowed businesses to stay open, so we expect everyone at the critical time to play their part."

Two flights are scheduled to arrive in Darwin on Wednesday with travellers to quarantine at the Howard Springs facility.

About 400 people are currently in the part of the facility managed by the NT government, with a further 500 international arrivals under the Commonwealth's supervision.

"Today's focus is alleviating that pressure in Alice Springs so that we can have capacity for any (arrivals), particularly road crossings," Ms Fyles said.

Australian Associated Press