Inmates in two prisons in south-east Queensland have started rooftop protests, with some of them angry about the newly enacted statewide prison smoking ban.

Five inmates climbed onto the roof of the Southern Queensland Correctional Centre at Gatton, west of Brisbane, this afternoon to protest against the ban that came into effect today.

Meanwhile, two inmates are also on top of the Arthur Gorrie Correctional Centre at Wacol, protesting over food and access to the exercise oval.

Both prisons were placed into lockdown as police negotiators talked to the prisoners.

State Attorney-General Jarrod Bleijie says jails started strictly policing the black market for cigarettes from today.

"In our prison cells, smoking has been banned since 2008 so to some extent they were already on the black market," he said.

"We'll be making sure that visitors are checked and that prisoners are not smoking."

Queensland's ban follows smoke-free rollouts in prisons in New Zealand and the Northern Territory.

The State Government says many prisoners have already chosen to quit in the lead-up to the change.

But Alison Finley-Bisset, from the Together Union, says it will create tension among inmates and staff in prisons already close to capacity.

"When that happened in New Zealand, with the same kind of factors in place, assaults on staff increased so significantly that they were in real strife there," she said.

"We are quite concerned with what overcrowding is doing in the prisons."