The rescue work at the site of the incident continued.
According to reports, people in the area who had woken for morning prayers heard cries for help and saw flames engulfing the top floor of the building, where children were sleeping in dorms.
The blaze at the Tahfiz Darul Quran Ittifaqiyah broke out around 5.40 am.
Roslan, a religious teacher, when asked about the students, spoke fondly of them.
He said the bodies were being identified via DNA tests as they had been severely burned and it would take some time.
Officials said fire engines were at the site within minutes, and the blaze was put out within an hour.
Police said the dead were 21 students - all boys between the age of 13 and 17 - and two staff members. Officials say that this is the worst fire disaster to strike the country in two decades.
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The Islamic "tahfiz" boarding school, where students learn to memorise the Koran, is in the Jalan Datuk Keramat area of the city. Students were also probably died due to the suffocation of the smoke inhalation. The investigation is going on about the cause of the fire accident.
He added that the dormitory only had a single entrance that left numerous victims trapped inside it. Amar Singh further said that "They're still counting the bodies, which were piled on top of each other in a corner." according to the official records, seven people were taken to a nearby hospital for injuries, while 11 others were rescued.
Fire officials said it appeared that the blaze was caused by a short circuit, but confirmation of this would only come following a forensic examination.
At least 15 bodies were found huddled together on another floor, it was reported.
"The sad part is during this incident, there is only one entrance to exit so the students were trapped inside", Singh said.
Such schools are not regulated by the education ministry of the country.
Dr Mahathir was referring to the fire at Taufiqiah Al-Khairiah Madrasa, also known as "Pondok Pak Ya", in Guar Chempedak, Kedah, which killed 27 female students on September 22, 1989.