An Israeli security source has told the BBC Israel was involved in the killing of a Hamas activist in Syria on Sunday.
Khalil had been in Syria since the early 1990s
Officially Israel has neither confirmed nor denied being behind the attack on Izz El-Deen Sheikh Khalil, whose car was destroyed by a bomb in Damascus.
Israel described him as a point man for the Palestinian Islamist movement's military actions in Gaza Strip.
Syria said Israel's attack showed its "intention to shake regional security and stability".
The Israelis had vowed to hit Hamas leaders "wherever they are" after suicide bomb attacks in August in Beersheba left 16 people dead.
Witnesses said they saw Mr Khalil get into his car and answer his mobile phone moments when the vehicle blew up. Three passers-by were injured.
Warning to Syria
Mr Khalil, 39, was a senior figure in Hamas' military wing and a member of the generation that set the group up.
He was based in Damascus along with other senior Hamas figures, including the overall leader, Khaled Meshaal.
He was among about 400 Palestinian militants deported by Israel to Lebanon in the early 1990s.
Israel has killed dozens of Hamas members in the last three years, including its two most senior leaders earlier in 2004.
Analysts say this latest Israeli assassination is intended to send a message to Syria's government that it will pay a high price for supporting Palestinian militant groups in the occupied territories.
Syria insists its support is political and not military.
BBC correspondent Barbara Plett says Syria's dilemma is how to respond.
Damascus cannot risk direct military confrontation with Israel, while indirect retaliation, through Hamas or another militant group, will only confirm Israel's accusations against Syria.
Our correspondent says Damascus will probably mount diplomatic protests, which are unlikely to do much to thwart Israeli action against it.