Speaking at the Biotechnology Industry Research Assistance Council's (BIRAC) foundation day, Reddy called for treading a cautious path on the issue as there has been difference of opinion among scientists and civil society.
"We are trying to build a consensus among various stakeholders like parliamentarians, NGOs, scientists and others. We will successfully arrive at a consensus very soon," he said.
Reddy said India cannot afford to completely abandon the GM crops as it needs to feed a growing population but has to proceed cautiously.
In 2010, the then environment and forests minister Jairam Ramesh imposed an indefinite moratorium on the commercial introduction of GM brinjal following several public hearings.
The Parliamentary Standing Committee on Agriculture, in a report August 2012, had asked for the banning of GM food crops in the country, while industry has been calling for their introduction to ensure food security.
The matter is also being heard in the Supreme Court.
More than 150 scientists wrote to the Environment and Forest Minister Jayanthi Natarajan last month, raising concerns about GM crops.
Their primary concern was that the agriculture ministry is allegedly making a case for GM crops by stating that the technology is absolutely needed for India's food security.
K. Vijay Raghavan, chairman BIRAC and secretary, department of biotechnology, said Indian needs to devise a good regulatory system and communication mechanism on GM food.
"We are a large country with social needs and need to carry technology research," he said.
Calling for building trust, credibility and delivering it safely, Biocon chairman and managing director Kiran Mazumdar-Shaw said: "The concerns on GM crops are unfounded and these needs to be answered. The moratorium on GM crops is affecting the whole sector."