The home minister said the government would nevertheless cooperate with the United Nations High Commissioner for Refugees (UNHCR) and other relevant worldwide agencies in line with their humanitarian policies to give aid to the ethnic group.
The home minister had also said that India would not violate any global law by deporting Rohingyas, as it was not a signatory to the UN Refugees Convention 1951.
"This flow out of Myanmar has not stopped yet, it's into the hundreds of thousands of Rohingya (who are) still in Myanmar, we want to be ready in case there is a further exodus", said the UN's under secretary-general for humanitarian affairs, Mark Lowcock, in a Friday press briefing in Geneva.
There may be up to 100,000 more people in northern Rakhine waiting to cross into Bangladesh, according to the International Organization for Migration.
With the number of refugees seeking shelter in Bangladesh exceeding 500,000, the Bangladesh government on Thursday declared its decision to identify the Rohingyas as "forcefully displaced Myanmar citizens".
The UN agencies earlier feared more than 14,100 Rohingya children were at risk of dying from malnutrition in wretched camps, as they were most vulnerable to the paucity of food, with 145,500 infants under five needing urgent intervention to stave off malnutrition.
Around 515,000 Rohingya have arrived in Bangladesh from Myanmar's western state of Rakhine in six weeks since the end of August.
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The World Health Organisation (WHO) has warned of a potential cholera outbreak among the Rohingya, saying the arrival of vaccines in the affected areas had been delayed.
Access to much of the area has been blocked by Myanmar authorities.
The Under-Secretary-General for Humanitarian Affairs called for unimpeded access, and said a United Nations team should be able to get on the ground in Rakhine in the next few days.
On reports of mass graves of Hindus found in the violence-hit region, Haque said, "This is part of ethnic cleansing".
United Nations -led aid bodies have appealed for $434 million over six months to help up to 1.2 million people - including 300,000 Rohingya already in Bangladesh before the latest crisis and 300,000 Bangladeshi villagers in so-called host communities.
Myanmar leader Aung San Suu Kyi has faced criticism for not doing more to stop the violence, although a military-drafted constitution gives her no power over the security forces.
The agreement was reached on Monday following talks between Bangladeshi Foreign Minister Abul Hassan Mahmood and Myanmarese government official Kyaw Tint Swe in Dhaka. The predominantly Buddhist Myanmar considers them Bangladeshi, but Bangladesh says they're Burmese.