Publicly, the issue has stirred barely a ripple in the Southeast Asian neighbours, underscoring their cultural and philosophical gap with the rest of the Muslim world, where it has triggered outrage.
But even some liberal Indonesians and Malaysians express resentment over the French magazine's crude caricatures of the Prophet Mohamed and the "Je suis Charlie" reaction, while vehemently condemning the jihadist massacre at its Paris office.
"No one can justify those killings. Our religion does not allow that," said Mr Zamfis Anuar, a Muslim primary school teacher in Kuala Lumpur.
But the reaction in the West "makes (Muslims) think, 'who are your friends?'"
The issue has emerged at a delicate time for Malaysia and Indonesia, the world's most populous Muslim country, with both nations on alert over Islamic State militants' proven ability to lure their citizens to jihad in Syria.
Many Muslims in Southeast Asia, like their counterparts elsewhere, believe a Western anti-Islam agenda exists, said Mr Noorhaidi Hasan, a lecturer on Islam at Indonesia's Sunan Kalijaga Islamic University.
"The Charlie Hebdo incident likely strengthens at some level their belief in that conspiracy theory," he said.
If coupled with worsening economic conditions, this could "give rise to radicalism", he added.
Frequently feted by the West as examples for the rest of the Muslim world, stable and economically dynamic Indonesia and Malaysia have centuries-old traditions of moderate Islam, which experts say are unlikely to change.
But some in Muslim-majority, multi-ethnic Malaysia have used the attacks to decry the West.
A conservative firebrand suggested the magazine had it coming, and popular Youth Minister Mr Khairy Jamaluddin called the post-attack anti-terror march in Paris by various world leaders "nauseating".
"Muslims are no longer talking about the attack but about the West's hostility. This can increase radical ideas," said Mohamad Asri Zainal Abidin, former official mufti, or Islamic scholar, for the northern Malaysian state of Perlis.
"Many Muslims may start to believe that there is no space for good relations with the West, which leaves no hope for moderates."
Some Malaysian officials, meanwhile, have sparked concern by using the episode to justify an ongoing crackdown on free speech that has dismayed progressives.
Both countries have warned of possible attacks at home by IS sympathisers, with Malaysian officials saying Charlie Hebdo could potentially escalate the threat.
by Dan Martin
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