Muslim leaders are fuming at what they claim is the unacceptable treatment of a senior cleric by officials at Sydney airport.

The imam was detained yesterday for two and a half hours by Customs officials for a routine baggage search at Sydney International Airport, which caused him to miss his flight.

He was on his way to Mecca in Saudi Arabia to perform the Hajj, and was travelling with a group of Australian pilgrims.

The manner in which the detention occurred was extremely unprofessional said the Grand Mufti of Australia, Dr Ibrahim Abu Mohammad, and leaders of a number of Muslim community organisations.

"It is totally unacceptable for any Australian citizen let alone a senior member of ANIC (Australian National Imams Council) to be subjected to this seemingly random yet profiled manner causing severe stress and unwanted inconvenience," said Dr Ibrahim Abu Mohammad in a statement today.

The incident exposes severe shortcomings with the process in place at Sydney's airport, they say.

After ASIO increased Australia's security threat level to high last week, the government said passengers would encounter delays at airports.

Comment was being sought from Sydney Airport.

Muslim leaders have called for calm after yesterday's counter-terrorism raids in Sydney and Brisbane which resulted in four people being charged.

One of the four, Omarjan Azari, 22, of Guildford, is accused of plotting to behead a member of the public in Sydney.

They want to "reassure all Australians that they have nothing to fear from their Muslim neighbours who want peace and security for everyone regardless of religion".

"We have a vested interest in the safety and security of Australia," Dr Mohammad said in today's statement.

The leaders noted a dramatic increase of abuse and discrimination against Muslim Australians in recent weeks, and said a Facebook page had been set up in response.

"We call on anyone who may have suffered a hate or bias motivated crime to call and contact the nearest police station and to report it using a special Facebook page that has been set up to register these incidents," the statement said.

An increase in abuse is a concern from all sides of the issue, with a Catholic nun at a Maronite school in Sydney's west threatened this week by a group waving an Islamic State flag reportedly yelling they would "slaughter the Christians."

The grand mufti said politicians and the media must not use the raids to inflame hatred of certain segments of the community.

Prime Minister Tony Abbott also called for tolerance.