There are long waits at the Federal Highway entrance into the ACT after police set up a check point at midday.

As of 3pm, police had stopped 820 vehicles and spoken to those in the cars.

Authorities have warned people will face "stiff penalties" for flouting the new rules.

From noon on Saturday, non-ACT residents who have travelled from COVID-19 affected areas of NSW require an exemption to be in the ACT.

People who are not residents of the ACT who have been in the Northern Beaches, Greater Sydney, Central Coast and Wollongong local government areas of NSW will not be able to enter the ACT unless they have been given an exemption.

Some cars have reportedly been denied entry into the ACT since police established the border checkpoint.

People attempting to enter the ACT just after midday reported long queues of up to three hours about a kilometre out from the border.

However by later in the afternoon, people reported being waved through the checkpoint, including those with NSW number plates, without being stopped.

ACT residents will still be able to enter the territory, but must notify ACT Health of their intention to return and enter 14-day quarantine if arriving after visiting any of the above regions.

Previous measures introduced on December 21 had allowed non-ACT residents who had been in NSW hotspots to enter the ACT and quarantine immediately, though it strongly advised against it.

ACT chief health officer Kerryn Coleman said the tighter restrictions were necessary to protect the ACT community.

"In recent days we have continued to see around 80 non-ACT residents from COVID-19 affected areas travel to the ACT daily," Dr Coleman said.

"As a result we now have around 2000 people in quarantine in the ACT, 25 per cent of which are non-ACT residents.

"We are putting in place strengthened travel restrictions to make it absolutely clear to non-ACT residents who live or have recently visited COVID-19 affected areas of NSW that they are not able to be in the ACT at this time."

She said she was concerned people had been flouting the rules.

"I think we've all heard anecdotal snippets about people potentially not doing the right thing and it's extremely disappointing and it puts the ACT community at risk," Dr Coleman said.

"Yes, I am concerned about it. This is like any other law that we have.

"We can't be on everybody every second of the day. It is people's responsibility to respect the law and I expect them to do that.

"This is my plea: we are all in this together and we desperately need people to understand the importance of this and do what we're asking them to do."

In a statement issued at 12.30am on Saturday, the ACT government said ACT Policing would have a presence at the Federal Highway to enforce the public health direction.

People seeking an exemption to enter the ACT for "extraordinary circumstances" will need to apply at least three days before their intended travel date, the statement said.

Speaking on Saturday morning, acting Health Minister Chris Steel said the government was working with ACT police on what other entry points would be patrolled.

"People need to know if they're from these affected areas ... and they come to the ACT they may be turned around at the border, and if they're found in the ACT they may face penalties of up to $8000 if they're found in the ACT without an exception," he said.

"If you are not granted an exemption by ACT Health you are not permitted to enter the ACT, do not come."

Detective Superintendent Rohan Smith said officers would be speaking to drivers to ensure they were aware of the new public health directions.

"For everyone's safety, it is important that drivers follow the signs to slow down as they approach the check point and listen to instructions from police officers," he said.

"Officers will ask people to leave the ACT if they are coming from a hot spot area and do not have an exemption.

"ACT Policing will continue to patrol highways and roads into Canberra, and will increase its activities at certain times of the day."

Canberran Belinda Duke returned from the South Coast on Saturday and reached the traffic a few kilometres out from the border about 1.45pm.

She said it took about two hours from that point to cross the ACT border.

"We knew the checkpoint was going up from 12 pm today but we didn't expect it to be like that," she said

"I think at one point we'd gone 200 metres in one hour.

"But the police were really good, they were very apologetic and were checking how long it was taking."

Current advice is different for ACT residents and non-ACT residents.

Firstly, check if any of the NSW areas you have been in are in the list of affected local government areas.

Non-ACT residents:

ACT residents:

Current quarantine advice:

The ACT government has advised ACT residents not to travel to the Northern Beaches, Greater Sydney, Central Coast and Wollongong local government areas until further notice.