"I completely deny the authenticity of this," Walid al-Mualem, Syria's foreign minister, told a news conference in Kuwait on Friday when asked about the militants' confessions aired on Jordanian state television on Thursday.
"We care for Jordan and ties are constructive between Syria and Jordan," Mualem added.
The exiled leadership of Hamas is based in Syria.
Jordan said on Wednesday that it had arrested 20 Hamas activists last month who were part of a plot to stage attacks in the kingdom.
On Thursday, two of the suspects said on Jordanian television that they were recruited by operatives from the Palestinian militant group's Damascus-based leadership.
The television showed rocket launchers that it said were part of an uncovered Hamas arms caches.
There was no way to verify the authenticity of the confessions. Independent lawyers and rights groups say many confessions by political detainees are extracted under duress.
Hamas has repeatedly denied accusations that its members are involved in arms smuggling to Jordan from Syria and refuses to join a committee set up by Mahmoud Abbas, the Palestinian president, to investigate the case with Jordanian officials.