Around 128 pupils and staff were evacuated yesterday from Darul Uloom School, in Foxbury Avenue, Chislehurst.
Two men were treated for the effects of breathing in smoke.
Metropolitan Police Commissioner Bernard Hogan-Howe said the force was "working tirelessly" to establish whether the blaze was started deliberately and urged the public to remain calm and not to speculate about the cause.
"Detectives are working tirelessly to establish whether these fires were started deliberately, and if so, to catch those responsible," Hogan-Howe said.
"We should not allow the murder of Lee Rigby to come between Londoners. These are difficult times for London's communities. The unified response we have seen to his death across all communities will triumph over those who seek to divide us," he said.
A school spokesperson, Sayed Mahmood, said he was "deeply saddened" and that intruders had been caught on the school's security cameras.
London Fire Brigade said there was minor damage to the building and 21 firefighters tackled the blaze.
The incident follows a rise in religious hate crimes after the killing of soldier Drummer Lee Rigby in Woolwich, south-east London, by suspected Islamist terrorists on May 22.
Last week, a Somali cultural centre and mosque was burned to the ground in Muswell Hill, north London, and the letters "EDL" - the initials of the right-wing English Defence League - were found scrawled on the outside.
The Darul Uloom School is 3,000 pounds-a-year boarding school which was established in 1988 with the purpose of producing "great scholars and 'Huffaz' (people who have memorised the Quran) to preserve and transmit the eternal message of Allah", according to the school's website.
Pupils and staff were able to return to the school building this morning.
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