No one is believed to have been hurt in the incident that took place at Harlow Islamic Centre in Paringdon Road in Essex.
"Detectives are investigating this concerning incident and there will be a significant police presence throughout the day to reassure all local residents as we seek to identify those responsible," Chief Inspector Ed Wells of Essex Police said today.
The mosque was set up 18 years ago when the Muslim community in Harlow grew in numbers and now serves a 2,000-strong community, according to the centre's website.
Zia Rehman, the Islamic centre's vice-chairman, said there had been a concerted effort to start a blaze.
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"Every entrance has been sealed with some kind of foam to allow the fire to take hold and set the building alight," he said.
Members of the mosque found the damage when they came in to pray in the early hours today.
The centre suffered limited damage and was hoping to re-open in time for people to attend prayers soon.