Christian Porter has warned Australian Capital Territory cannabis users they may not be protected by a new law legalising recreational use, weighing in alongside the home affairs minister, Peter Dutton, against the law.

On Thursday Dutton described the new laws as unconscionable, comments interpreted as urging the attorney general to challenge or overturn the ACT law, passed on Wednesday.

“I think it might be trendy for the ACT government to go down this path, and they’ll say they’re enlightened and progressive and all the rest of it,” Dutton told 2GB radio. “But I think it’s dangerous … Christian Porter is having a look at it at the moment.”

Porter played down – but did not rule out – the possibility of the commonwealth directly overriding the laws. He told Guardian Australia the laws are “obviously a matter for the ACT” and he will consider “what issues may arise to the enforcement of existing commonwealth laws that criminalise the possession of prohibited drugs, including marijuana”.

Porter told 6PR Radio he “[thinks] this is a very bad idea” but argued cannabis possession was “very different” from instances where the commonwealth had intervened to override the ACT on same-sex marriage and euthanasia.

Porter warned it was an “open question” whether the ACT parliament had successfully overridden existing commonwealth offences.

“If you’re in the ACT waking up today and you want to possess marijuana, be careful, because there are commonwealth laws that still apply,” he said.

He would ask the Australian federal police its view but if the commonwealth laws still applied “the expectation would be commonwealth laws would be enforced”.

The laws allow residents over 18 to possess up to 50 grams and grow two plants. Under existing legislation, people with up to 50 grams or two plants for personal use face fines. If paid within 60 days, they will not appear on a criminal record.

ACT’s chief minister shrugged off concerns Canberrans would be targeted by federal prosecutors when the scheme comes into effect in January. The territory’s police had been balancing the overlap with commonwealth for nearly three decades, Andrew Barr said.

“Does anyone seriously think the commonwealth DPP [director of public prosecutions] is going to spend all of their time, or a considerable amount of their time, prosecuting individuals in the ACT for the possession of less than 50 grams of cannabis?” he told ABC’s Radio National on Thursday.

“It’s one thing for police to arrest someone, it’s another thing to successfully prosecute someone.”

The existence of the ACT legislation was a defence if people were charged under commonwealth laws, Barr said. “My advice to everyone is that this is an evolution not a revolution,” he said.

Barr’s position had support from the commonwealth director of public prosecutions, Sarah McNaughton, who wrote to the ACT government on 17 September suggesting the commonwealth law provided a defence for people engaged in conduct “justified or excused” by a state or territory law. McNaughton also noted the commonwealth director of public prosecutions would consider the defence when deciding whether to press charges.

But on 22 September McNaughton withdrew her earlier advice, suggesting there were further unspecified “legal complexities”, declining to give a view on whether the ACT law could protect residents from commonwealth charges.

On 23 September the attorney general’s department’s deputy secretary, Sarah Chidgey, agreed the ACT law could provide a defence but warned the “justification or excuse may need to be more explicitly identified” in the bill.

The territory’s shadow attorney general, Jeremy Hanson, thinks the legalisation was sending the wrong message, citing research showing marijuana’s link to psychosis.

Hanson was concerned it would lead to more drug driving and did not believe the laws were enough of a deterrent. But he did not expect the federal government to test the overlap in the courts.

“A greater concern is an individual out there thinking they’re doing the right thing, thinking they’re doing something legal, and finding themselves being charged with a commonwealth offence,” he told Sky News.

“The reality is we had a pretty good regime up until yesterday. It’s not like people were being thrown into jail for cannabis use holus-bolus.”