Deputy Foreign Affairs Minister Datuk Seri Reezal Merican Naina Merican said the government decided to evacuate the students when the Air Pollution Index reading touched 980 on Sept 14.
An API of over 300 is considered hazardous.
"It is a normal evacuation process under such circumstances. We are glad that it went smoothly and the Indonesian government was very cooperative," Reezal said after receiving the students at the Royal Malaysian Air Force airbase in Subang on Friday.
Reezal said there was no report of serious illness among the students.
"As far as we know, there has not been any case of illness caused by the haze. Everyone looked to be in good spirits but I can't say for sure," he said.
The first batch of 120 students from State Islamic University of Sultan Syarif Kasim and Pondok Pasentren Al Baidha arrived on Thursday.
The ministry had also provided buses to Kuala Lumpur Sentral, TBS and Pudu Raya where the students can take buses to return to their hometowns.