Abdul Hadi Awang, president of the Pan-Malaysian Islamic Party, said his party was against all acts of terrorism but not fully convinced that Azahari shot dead by Indonesian police last week had masterminded the attacks.
"I fear that the allegations against Azahari could be like the allegations made against Iraq (possessing weapons of mass destruction)," Abdul Hadi told reporters.
"Until today, there is no proof (of Azahari's involvement). We want a fair investigation into the allegations," he said.
Azahari, a former university lecturer and alleged explosives expert, was accused of helping coordinate four deadly strikes by the al-Qaida-linked Southeast Asian terrorist group Jemaah Islamiyah in Indonesia since 2002, including last month's Bali bombings.
He has spent the last three years on the run.
Abdul Hadi said there has not been sufficient proof to back the accusation, which he claimed was made based on media reports and allegations by the United States.
"We should not bow down to the United States' imperialist agenda," he said.
Abdul Hadi stressed, however, that his party supported the efforts taken by the Malaysian government to fight terrorism, and has been telling its members that killing civilians was wrong.
"In principle, we condemn all acts of terrorism," he said. "If any of our members are found to be involved in terrorist activities, we will sack them."
Jemaah Islamiyah wants to establish an Islamic state spanning Indonesia, Malaysia, Singapore and the southern Philippines. But it has been weakened in recent years by a regional crackdown that has resulted in dozens of arrests, reported AP.