"However our current regime for regulating new organisms is highly restrictive in practice, which means we do not have the flexibility to choose whether this is something we would want in New Zealand.
Mr Makhlouf said the regime also denied New Zealanders the choice to adopt new plants and species that offered huge advantages, such as drought-resistant rye grass.
The Ministry for the Environment also believes the rules for genetically modified organisms needed to be reviewed.
In a briefing to Environment Minister Nick Smith last year, the ministry said "it is critical that decision-making parameters keep pace with advances in science and technology that can alter the risk profile of hazards".
Prime Minister John Key yesterday(MON) played down the chances of a change in GM rules, and said officials had been lobbying on this issue for some time.
"The point that I would simply make is that it's complex. It's quite an emotive area and it would be really important that people would understand the issues as and if we went to either change or debate those issues."
He added: "There is certainly a belief from some people that we could make moves in that area that would be improved in legislation. But equally there will be a lobby of people strongly opposed to that."
Federated Farmers welcomed Mr Mahlouf's comments, saying it was time for new debate on the issue.
President William Rolleston said: "Our laws in this area, which discriminate on technology rather than on risk are no longer fit for purpose and are denying New Zealand farmers the choice they would otherwise have."
GE Free New Zealand said the only six GM field trials approved in the last decade had cost millions and produced "no results that show they will have a better outcome than their conventional counterparts".
"In fact, they have shown they are extremely toxic cruel failures," the lobby group said.
At present, GM applications are regulated by the Environmental Risk Management Authority.
The number of applications for trials has dropped significantly since a law change relating to hazardous substances came into effect in 2001.
Research institutes have also complained of high application costs, often up to a $1 million or more.