Three men will be charged with serious terrorism offences following arson attacks that destroyed an Islamic Centre in Melbourne's northern suburbs.

Police will allege in court that last-year's fire-bombing of the Imam Ali Islamic Centre – a building used by Shiite Muslims – was a sectarian attack that was inspired by Islamic State.

Two of the men facing terrorism charges are already in custody over their alleged involvement in a plot to bomb Melbourne's Flinders Street Station, Federation Square and St Paul's Cathedral on Christmas Day 2016.

Hatim Moukhaiber, 29, of Meadow Heights was arrested on Saturday night by members of the Special Operation Group, after his vehicle was pulled over in Roxburgh Park.