Police established a checkpoint on the Federal Highway near the border on Saturday after the ACT government announced it was effectively closing its borders to non-residents who had been in one of NSW's coronavirus hotspots.

However, there were no checks on motorists arriving on other major highways into the ACT, including the Barton Highway and Kings Highway.

Dr Coleman defended the approach on ABC Radio on Monday.

"As we have talked about before, we are not doing a hard border closure with NSW ... it just doesn't make sense to do that," Dr Coleman said.

"So we are really trying to focus efforts where the greatest risks is and where the greatest number of people come back."

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There were almost 2700 people quarantining in the ACT as of Sunday afternoon, with 2523 of them having returned from NSW COVID-19 hotspots. Dr Coleman did not have updated figures on Monday morning.

The Federal Highway's checkpoints caused confusion and frustration for many on Saturday as queues along the major highway stretched on for kilometres.

One resident, Simone Maher, visited Lerida Estate to celebrate a birthday lunch with friends on Saturday. On her return, she was caught in a long line of cars waiting to enter the territory, making the typically 30-minute journey into a three-hour one.

"We were not aware we would be stopped by [a] checkpoint coming home," Ms Maher said.

The stoppage started around 1.5 kilometres out from Eagle Hawk Park, Ms Maher said. Once she made it to the police checkpoint by 5.30pm, her licence was checked and a few questions asked and she was allowed to pass through.

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