"We regret Bashar's recent attack on [Hamas political chief] Khaled Meshaal," Abu Marzouq wrote on his Facebook page on Sunday.
Last week, Assad said that Syrian security forces had detained Meshaal's daughter and wife for an alleged attempt to smuggle weapons to Syrian opposition forces.
He said that the pair had later been released after mediation from Hamas leaders.
Assad also said that Hamas had tried to mediate between the Syrian regime and the Muslim Brotherhood group, but Damascus had rejected the move.
Abu Marzouq denied claims that Meshaal's wife and daughter had smuggled weapons to the opposition, saying that the pair had never provided support for the Syrian opposition during their presence in Syria.
The Hamas leader went on to say that Meshaal's attempt to mediate between the Muslim Brotherhood and the Assad regime was at the Brotherhood's request.
"Meshaal had always been critical of Syria's Muslim Brotherhood group for their differences with the [Syrian] regime, not as reported by the President," he said.