"The government will go according to the policy to deal with refugees ... when the situation is good enough for them to return to their country," he told reporters in Thiruvananthapuram.
Nobody wants to stay as a refugee, the minister of state for external affairs said.
Minister of State for Home Affairs Kiren Rijiju had on September 5 said the Rohingya were illegal immigrants and stood to be deported.
The Rohingya, a stateless Muslim minority, are regarded as illegal immigrants in Myanmar. Thousands of them have fled to Bangladesh and India.
Around 40,000 Rohingya Muslims have settled in India, and nearly 16,000 of them have received refugee documentation, according to the United Nations.
UN human rights chief Zeid Ra'ad Al Hussein had on Tuesday accused Myanmar of waging a "systematic attack" on the minority.
Asked if India was hopeful of bringing back former Naval officer Kulbhushan Jadhav, sentenced to death by a Pakistani military court on the charge of espionage, he said some matters were being handled "very delicately and there is no point in putting out anything till things solidify".
India had on May 8 taken the Kulbhushan Jadhav case to the International Court of Justice, accusing Pakistan of violating the Vienna Convention and conducting a "farcical trial".
The International Court of Justice had stayed the execution of Kulbhushan Jadhav.
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