Ayman al-Zawahiri, the deputy leader of al-Qaeda, has accused Hamas of "submission" for agreeing to form a Palestinian national unity government.
Al-Zawahiri said Hamas had "fallen into the swamp of surrender" by accepting a Saudi-brokered deal with the US-backed Fatah faction in Mecca, in an audio recording broadcast by Al Jazeera on Sunday.
"The leadership of Hamas surrendered to the Jews [and] most of Palestine" in order to keep leadership of the Palestinian government, he said.
Hamas and Fatah agreed a month ago to forge a coalition cabinet, largely ending factional fighting centred in Gaza where more than 90 people died.
Zawahiri said: "Hamas has sold out so it can keep a hold of a third of government.
"But what government? A government that doesn't even have the right to enter or leave [the Palestinian territories] without Israeli permission."
He said: "The leadership of Hamas government has committed an aggression against the rights of the Islamic nation by accepting what it called... respecting international agreements.
"I am sorry to have to offer the Islamic nation my condolences for the [virtual demise] of the Hamas leadership as it has fallen in the quagmire of surrender."
Hamas, which came to power in January 2006, refuses to recognise Israel.
Their stance has led to Western countries boycotting the Palestinian government, led by Hamas after its electoral win in January 2005.
His comments were broadcast as Ehud Olmert, the Israeli prime minister, and Mahmoud Abbas, the Palestinian president and head of Fatah, were reported to have made little progress during talks on key issues in Jerusalem.
The two men met in Olmert's official residence on Sunday hours after violent clashes took place between Hamas and Fatah fighters in Gaza.
Olmert has already said he will boycott any unity government that fails to recognise Israel's right to exist.
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But he also promised to keep channels of communication open and officials said more talks between the two men were likely to take place.
Olmert and Abbas last met on February 19 in trilateral talks with Condoleezza Rice, the US secretary of state, that ended with no sign of progress towards resuming peace talks that ended six years ago.
The unity deal, reached last month in the Saudi holy city of Mecca, only agrees to "respect" past agreements, falling short of international conditions.
"The Israeli government has expressed its disappointment over the Mecca accord and has not changed its position," Olmert told his cabinet before the summit on Sunday.
"We hope that the Palestinian government that is to be formed will accept the Quartet [international] principles."