The commission set the precedent last year by approving pokies in a smoking area at a Wellington pub.
That ruling overturned the separation of smoking and gambling which became established with the extension of smokefree workplace law in 2004, even though the smokefree and gambling acts say nothing about smoking while gambling.
Under the smokefree law, any smoking areas at pubs and casinos have to be open to the outdoors.
Public health groups have condemned the commission rulings.
They say 58 per cent of problem gamblers are smokers, and having to go to a non-pokie area for a smoke is a gambling circuit-breaker for many.
It gives them a chance to reflect on how long they have been gambling and how much money they have lost.
Professor Abbott said that although there was no formal research on the effect of smoking bans on problem gambling, such bans in New Zealand and Victoria had been followed by a reduction in spending on pokies and in calls to problem-gambling help services.
"The smoking ban might have been the most effective harm-minimisation measure yet in New Zealand [for problem gambling]."
But the commission said Auckland casino operator SkyCity told it that despite the perceived benefits of breaks in play, "it has no evidence to indicate that at-risk gamblers who smoke would be more likely to take a break if prevented from smoking while gambling".
SkyCity said pokie players were already regularly interrupted by pop-ups on the machines that gave information including how much the gambler had lost.
The commission concluded the research did not establish a clear reduction in problem-gambling harm from banning smoking while gambling.
Problem Gambling Foundation chief executive Graeme Ramsey said Australian research indicated 40 per cent of spending on pokies was done by people with a gambling problem.
"This move seems like a means to keep people at machines and extract more money from that same group."
Action on Smoking and Health director Ben Youdan said Ash was concerned by two dangerous practices being "wrapped up in one quite harmful package".
CHANGES
* The Gambling Commission has permitted pokies in smoking areas at the Auckland and Dunedin casinos.
* People will be able to smoke while they play the pokies.
* Under the smokefree law, any smoking areas at pubs and casinos have to be open to the outdoors.