While giving his nod, Moily, however, sought to downplay the approval row, saying there was some "misunderstanding" over the issue and there was no "embargo" from Supreme Court on such trials.
The minister's nod will pave the way for GM field trails for rice, wheat, maize and cotton.
Moily, however, made it clear that the trials are subject to approval by state governments and fulfilment of certain conditions.
The clearance will enable companies such as Bayer Bioscience, Mahyco and BASF and Monsanto India to carry out field trials for the crops. Bayer Bioscience, for example, has been given clearance to test GM rice across the country.
Earlier, Natarajan had blocked the approval obtained by GEAC in March of last year, reportedly because the issue was pending in the apex court.
But Moily said he had examined the case with officials and found that there was no embargo on the clearance by Supreme Court, Moily said.
"It is a report from a statutory committee. I don't think a ministry or a minister will have any business holding it back. We can't do that. We have to work with the rules... and the law of the land is same for everyone. That is why, as a law-abiding minister, I approved it," Moily told reporters here.
The minister also said that the Environment Ministry, Agriculture Ministry and the Department of Biotechnology had a "common position" on the issue, which would be placed before Supreme Court.
Natarajan had, in fact, not "disagreed" with the decision of the GEAC, he further stated.
The next meeting of GEAC has been called on March 21 to discuss some more issues, he said.