Mahmoud Abbas has threatened to break off a unity agreement with Hamas if the movement does not allow the government to operate properly in the Gaza Strip.
Speaking in Cairo ahead of an Arab League foreign ministers' meeting, the Palestinian president accused Hamas of running a shadow government and said he wanted a single authority and a single system of rule.
"We will not accept the situation with Hamas continuing as it is at the moment," Abbas said on arrival in the Egyptian capital late on Saturday, in remarks published by official Palestinian news agency WAFA.
"We won't accept a partnership with them if the situation continues like this in Gaza where there is a shadow government ... running the territory.
"The national consensus government cannot do anything on the ground," he charged.
His comments came nearly two weeks after a ceasefire ended a deadly 50-day confrontation with Israel in Gaza.
Abbas also accused Hamas of undertaking executions without trial.
Hamas denounced his allegations as baseless.
"Abbas's statements are unjustified," spokesman Sami Abu Zuhri said. "It is untrue, baseless and unfair to our people."
Abbas appeared on the verge of another public attack on Hamas in the opening of his address to the Arab League on Sunday. However, journalists were ordered out of the room 30 seconds into his speech.
Al Jazeera's Mike Hanna, reporting from Ramallah, said: "The remarks were clearly designed as warning shots across the bow.
"Abbas is intent on getting Hamas to give up a degree of control within Gaza, control that he says is being abused."
Under the terms of the reconciliation deal earlier this year, the factions agreed to form an interim consensus government and end seven years of rival administrations in the West Bank and Gaza.
The deal sought to end years of rivalry between Hamas and Fatah.
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The new cabinet, which is based in Ramallah, took office on June 2, with Gaza's Hamas government officially stepping down the same day. Hamas is however the de facto power in Gaza.
Khaled Meshaal, the Hamas leader in exile, said Palestinians should steer away from triggering problems in the media.
"I call on Abbas, Fatah, Hamas and all Palestinian factions and forces, including independent figures, to meet at the earliest, and come to an agreement in order to conclude our unity and the way forward ... one voice, one decision, one authority and one goal."
Source: Al Jazeera and agencies