"I stress to you once again: the Syrian army has not, did not and will not use this kind of weapons - not just against our own people, but even against the terrorists that attack our civilians with their mortar rounds," he said.
Muallem spoke at a press conference in Damascus two days after a suspected chemical attack left at least 86 people dead in the rebel-held town of Khan Sheikhun in northwestern Syria.
The deaths have sparked international outrage with many pointing the finger at the government of President Bashar al-Assad, but Muallem cast doubt on the evidence.
"The first air raid conducted by the Syrian army was at 11:30 am (0830 GMT) on that day (Tuesday) and it attacked an arms depot belonging to Al-Nusra Front that contained chemical weapons," he said.
Al-Nusra - now known as Fateh al-Sham Front - was once Al Qaeda's Syria affiliate and is the main terror rival of the ISIS.
"Al-Nusra Front and ISIS and other organisations continue to store chemical weapons in urban and residential areas," Muallem added.
The Syrian army denied on Tuesday that it had used chemical weapons against the town, and Damascus ally Moscow said "toxic substances" may have been released when the army struck a "terrorist warehouse".
The United Nations Commission of Inquiry on Syria and the Organisation for the Prohibition of Chemical Weapons (OPCW) both said they were investigating the attack. Britain, France and the United States have drafted a UN resolution that would demand Syria provide information on its flight operations as part of an OPCW probe.
On Thursday, Muallem said such an investigation "must guarantee that it is not politicised, that it has broad geographic representation and that it is launched from Damascus, not Turkey."
"We provide the OPCW and the UN with intelligence on the transfer of chemical substances from Iraq and into Syria, or from Turkey into Syria, but an investigation is for the OPCW," he said.