Investigators are trying to determine what caused a small fire at a controversial Auckland mosque early this morning.

The fire was in a storage area attached to the side of the main building at the west Auckland Islamic Centre in Avondale but the Fire Service told ONE News the damage could have been much worse.

Initially two fire trucks attended the scene at around 3am and as a precaution an additional two fire trucks also attended.

Senior Sergeant Greg Sowter said the building has been cordoned off while they hunt for clues as to what caused the fire.

"The fire is being treated as suspicious," he told ONE News. "It's not very bad...but it was just starting."

Detective Senior Sergeant Paul Newman from Glenn Innes CIB said damage was limited to the inside of this a shed.

"Thankfully, a member of the public noticed smoke and call for assistance...the mosque itself was not damaged," says Mr Newman.

Police and the Fire Service are combing the property in a bid to find out how the potentially destructive blaze started in the empty building.

"We've got our specialist fire investigators looking at it now and we'll be sending some material away for testing. We won't know the results of that for at least 48 hours," Assistant Area Commander Dave Woon said.

Hours before the blaze people had been at the centre cleaning the mosque and people who run the centre told ONE News the fire was most likely an accident caused by them.

But a long term leadership struggle and violence saw the mosque close its doors in May.

An administrator - the former president of the Muslim Association - was beaten up and taken to hospital. Before that others were banned for "inciting disharmony" and one of them, Sheikh abu Abdulla, began leading his own Friday prayers from his garage.

But the Muslim Association does not believe they dissenters would attempt to burn down the mosque.

"I don't think so because this is a place of worship, this is a church, this is a mosque, this is a place of worship for the community," Firoz Patel said.

"There is no benefit to doing an act like that."