In Cairo, Condoleezza Rice, the US secretary of state, justified the arming of Fatah, saying the situation had called for it.
She said she had not read a report in Vanity Fair magazine which quoted a former US intelligence official said to be knowledgeable of the US plans to overthrow Hamas after it failed to convince Abbas to dissolve the cabinet.
"It is very clear that Hamas is being armed. And it is very clear that they are being armed in part by the Iranians," Rice said on Tuesday.
"So if the answer is that if Hamas gets armed by the Iranians and nobody helps to improve the security capabilities of the legitimate Palestinian Authority security forces, that's not a very good situation."
Rice said that international forces, including the US, would therefore continue to work with the PA to bolster its forces to keep security in its mandated region.
Responding to Rice's comments about Iranian support for Hamas, Khaled Meshaal, the exiled Hamas political leader, told Al Jazeera Rice was "lying".
"Their main concern is to provoke Iran," Meshaal said. "I'm saying it again if they have proof of this let them produce it".
"Everyone knows the origins of the Israeli weapons, it's American made while our men are using very simple homemade arms," he said.
The US has openly supported Fatah and after Hamas seized control of Gaza in June 2007, the US announced an $80m funding deal for Fatah's security services in the West Bank.
Nour Odeh, Al Jazeera's correspondent in Ramallah, said that many Palestinians would be upset that Fatah appeared to have played into the hands of an American foreign policy that wanted to make an example out of Hamas, whom the US labels a "terrorist" organisation.
Hamas won democratic elections in January 2006, prompting Western governments, which have refused to engage with Hamas, to threaten to withdraw financial aid to the Palestinians.
Left with little international support, by June that year Hamas and Fatah had agreed to form a unity government but were unable to broker a conclusive end to factional fighting on the streets of Gaza.
Allegations the US sought to remove Hamas in a coup dates back to 2006, after the group had come to power through Palestinian elections.
The leaked documents include a memo sent to Fatah officials, apparently by a senior US diplomat in Jerusalem in November 2006, encouraging Fatah to declare a state of emergency and take control.
The memo stated: "If Hamas does not agree [to accept a new government] within the prescribed time, you should make clear your intention to declare a state of emergency and form an emergency government explicitly committed to that platform."
The plan was ignored by Abbas who instead formed a unity government with Hamas in 2007, intended to bring an end to fighting between the two factions.
prompted the second document and a plan to oust Hamas by force, with the
The unity government, agreed in February 2007 with the mediation of Saudi Arabia, appears to have
US bolstering Mohammed Dahlan, the head of Fatah's security forces.
But the unity government failed to end
and in June Hamas seized Gaza, dividing the Palestinian territories into Gaza and the Fatah-controlled West Bank.
The US on Tuesday denied the coup plot allegations.
"There is no accuracy to that story. I've checked and there is no truth to it," Sean McCormack, the US state department spokesman, said.
A statement from the office of Mohammad Dahlan, the former head of the Palestinian national security council, called the Vantiy Fair article "highly inaccurate and misleading".
"Accordingly there was (and remains) no secret plan to carry out a coup against Hamas," said the statement.
"Although the US offered its financial support for the plan to reform the PA's [Palestinian Authority's] security forces (by offering assistance for non-lethal equipment as requested by the PA), financial support was never received."