"The prime minister has directed the two ministers to sit together and discuss the matter and sort out differences," Science and Technology Minister Kapil Sibal told reporters after the cabinet meeting.
He said the cabinet deferred a decision on the issue which was being argued before the court.
The Delhi high court is hearing a Public Interest Litigation challenging the legality of Section 377 of the Indian Penal Code which bans sexual relations among the people of the same gender.
"Whatever the court decides, we will agree," Sibal said.
The court had on Wednesday pulled up the Centre for relying on religious texts to justify the prohibition on gay sex in the country and asked it to come up with scientific reports to justify it.
The issue has become controversial with Ramadoss saying that he would take up the matter with the prime minister after his ministry was ticked off by the home ministry before the court.
The home ministry is opposing the health ministry's suggestion for legalising homosexuality.
The home ministry has suggested not to decriminalise gay sex on moral grounds while the health ministry has proposed to abolish the penal provision which carries a punishment of up to life imprisonment for such acts.
The health minister had sought legalisation of homosexuality arguing tat it can help in better treatment of people suffering from HIV/AIDS.
The National Aids Control Organisation, in its affidavit filed on behalf of Union health ministry, had said that gay sex among consenting adults should be decriminalised.
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