Territory taxpayers have subsidised an estimated $2.6 million for quarantined hot spot travellers to come to the Northern Territory and then move on to other states for holidays after exiting mandatory quarantine.

Chief Minister Michael Gunner said the cost to the government of mandatory two-week quarantine was around $3300 to $3400 – more than the $2500 currently charged to hot spot travellers.

Despite setting the price as a deterrent to people to come to the NT, nearly 63,000 people have come since July 17.

Government figures show 3080 people have been quarantined for two weeks in either the Howard Springs facility near Darwin or the Alice Springs facility.

The $2.6 million taxpayers will pay is based on the average difference of $850 per person.

Mr Gunner on Thursday acknowledged that many people were using the NT’s quarantining facilities to then travel to other states that would have previously banned them from entering from their home state.

“We at the moment are probably charging slightly less than we should and we might be subsidising other states’ quarantine arrangements,” Mr Gunner told ABC Radio.

“There are people coming through here to go to Queensland. We are looking at whether the Australian Government steps in or whether we maybe change some of our measures.

“We are offering essentially a national service at the moment.”

He added that discussions are ongoing with the Federal Government about using the facilities here for possible future federal purposes, but did not provide details of what that would look like or how much it would cost taxpayers.

Mr Gunner said the $2500 fee was an arbitrary estimate they came up with in April before knowing the actual cost and suggested the rate could change.

Mr Gunner said the cost was supposed to deter people from coming but admitted people were now attracted to the NT, so they can then move elsewhere.

He did not say when the costs would be changed.