State officials said no one was injured and no damage caused in the early-morning attack after the firebomb landed on the centre's metal shutters.
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State Deputy Chief Minister P Ramasamy said the attack may have been prompted by his Facebook post over the weekend about Zakir Naik. "It could possibly be related to my comment on Zakir as Satan," he told AFP.
Ramasamy accused Zakir, an Indian national, of giving speeches designed to promote hatred of other faiths. His posting was not directed against Islam or Muslims but against "this particular person", he said in a statment.
"I regret the use of the word 'Satan' which has caused uneasiness and unhappiness among Muslims in Malaysia," Ramasamy said, adding that the word was later deleted.
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Malaysia generally practises a moderate brand of Islam among its majority Malay community, but conservative views have gained increasing traction in recent years. Minorities -- mainly ethnic Indians and Chinese -- complain of what they see as Islamisation.
Religious tensions escalated in 2010 after three churches were attacked with firebombs, causing major damage to one, as Muslims pledged to prevent Christians from using the word "Allah". Zakir, 51, is an Islamic preacher on comparative religion.
Ramasamy, who is also the Penang Hindu Endowment Board chairman, had spoken out against a planned programme by Zakir's son, also an Islamic preacher, in Penang state on April 15.
On Sunday police banned Zakir from giving a lecture at a university in the southern state of Malacca following complaints from minority groups. He had planned to speak on "Similarities between Hinduism and Islam".
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National police chief Khalid Abu Bakar said in a tweet on Monday that Zakir was barred to ensure public order. The aim was to protect "public order and religious sensitivities in Malaysia", he wrote.
Issues related to race, religion and language are considered sensitive in Malaysia, which witnessed deadly riots mainly between ethnic Malays and Chinese in 1969.
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