Five fire engines tackled the blaze at the Nasfat Manchester Islamic Centre on Droylsden Road in the northern England city and Greater Manchester Police (GMP) said they are treating yesterday's incident as "suspicious".
"We sent five pumps to the scene and an investigation is now underway. The fire is being treated as suspicious and a joint investigation has been launched by GMP and GMFRS (Greater Manchester Fire and Rescue Service)," a GMP statement said today.
Nasfat (Nasrul-Lahi-l-Fathi Society of Nigeria) opened up in Manchester as a mosque and Islamic centre in 2009 and it has about 300 members.
Monsurat Adebanjo-Aremu, secretary of the centre, told Manchester Evening News that yesterday's fire was the third such major fire incident in a year.
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She said people have also urinated outside.
The mosque has previously been targeted with two pigs' heads thrown into the building while people were praying and a minibus was destroyed in an arson attack in 2014.
In the latest attack, pictures from the scene show flames erupting from the roof of the single-storey building.