Crowds had gathered at the city's airport to welcome Tahirul Qadri from Canada where he lives, but his flight was diverted to Lahore.
He says he plans to lead a crusade against corrupt politicians.
At least eight people were killed last week when police in Lahore used tear gas and bullets against his followers.
Police had sealed off roads to Islamabad airport but some of the cleric's supporters - chanting "Islamic revolution" and "long live the army" - managed to break through the security cordon.