Israel's intelligence and special operations force, Mossad, sent a team to the Syrian capital in July to carry out the killing, Hamas sources said on Wednesday quoting "Western intelligence sources".
Khalid Mishaal is living in exile in Damascus.
Mossad agents allegedly posed as volunteers for relief organisations visiting Syria to help refugees from the war in Lebanon, the sources added.
Aljazeera has learnt that Mishaal has stepped up his personal security since the plot.
Shimon Peres, the Israeli vice-prime minister, has accused the exiled Hamas leader of ordering the raid during which an Israeli army reservist was captured.
The capture of Gilad Shalit on June 25 lead to Israeli forces moving back into the Gaza Strip.
Mishaal cannot visit Gaza or the West Bank but he is also not subject to Israel's travel restrictions on Hamas members and has played an important role in representing the government at meetings with foreign governments.
In 1997, Mishaal survived a botched assassination attempt while he was living in Jordan. Mossad agents disguised as Canadians injected poison into his ear in the street, but two of the agents were caught.
King Hussein of Jordan demanded the antidote to the poison in exchange for the return of the Israeli agents.
Mishaal became the leader of Hamas after Israel killed the group's founder, Sheikh Ahmad Yasin, in March 2004.