Local council officials said a church which had enraged Muslims with a cross it put on its facade was not licensed to operate at its address, while a number of prominent individuals and groups have slammed the protesters for being intolerant.
According to officials of the Petaling Jaya City Council, the church in Taman Medan has not submitted a written application to operate as a place of worship at the shoplot that it occupies.
Therefore, it also had no permit to put up a cross on its building, they added.
On Sunday, a group of 50 residents gathered outside the church to protest against the cross displayed on its building, claiming that it challenged Islam.
The group demanded the church take down the cross. It was removed on the same day.
Responding to the city council's claim, Selangor executive councillor Elizabeth Wong said yesterday that since 2008, all churches in the state only needed to notify the Committee on Non-Islam Affairs before starting operation.
The statement about churches having to apply for permits was therefore not accurate, according to Ms Wong.
She also said the government of Selangor found the forcible removal of the cross abhorrent to Christians and the Federal Constitution, which enshrined the freedom of worship.
Meanwhile, a number of Muslim leaders, non-governmental organisations and moderate Malaysians have criticised the residents' protest.
Perlis mufti Mohd Asri Zainul Abidin said "Islam does not teach its followers to disrespect other religions or disrupt their practices".
Chief executive Saifuddin Abdullah of Global Movement of Moderates, which campaigns for moderation as a way to realise world peace and harmony, said Islam upheld freedom of religion, but the "recent action by some quarters" was sending a different message.
The Muslim Professional Forum, which works to correct "misunderstandings" of Islam, said "(the) mindless act of hatred and incitement against another religion's place of worship had no place in Islam".