Suthep said the boat people were entering the country illegally and "we will not allow them to live here".
He denied fresh allegations of abuse after a second group of nearly 200 Rohingya migrants were found off Aceh province on the Indonesian island of Sumatera.
The discovery came a month after fishermen found a group of about 170 who said they had been cast adrift.
Many had severe injuries they said were the result of beatings from the Thai military.
An estimated 800,000 Rohingya, a stateless Muslim ethnic community from Arakan state in Myanmar's northwest, claim persecution by the military government and have fled to neighbouring countries in the region.
Those who ended up on Thai and Indonesian shores have alleged serial abuse by the Thai military.
Last month, the Thai military admitted towing hundreds of Rohingya migrants far out to sea before abandoning them, but insisted they had food and water.
They also denied reports that the engines were removed from the boats that were sent adrift.
According to the UN High Commissioner for Refugees, 230,000 Rohingya now live a precarious, stateless existence in Bangladesh, having fled decades of abuse and harassment at the hands of Myanmar's military rulers.