Mahmoud Abbas told delegates at a meeting attended by Hamas and his own Fatah movement on Tuesday that he would give them up to 10 days to reach agreement before calling for a popular vote.
Abbas said: "If you do not reach agreement by then, I would like to tell you frankly that I will put this document to a referendum. This is not a threat."
The plan was drawn up by members of both Fatah and Hamas who are jailed by Israel.
It calls for resistance to the continuing Israeli occupation, but allows for a negotiated settlement if Israel withdraws fully from West Bank land it has occupied since 1967. It would involve Israel removing all settlements from the West Bank.
It also calls for a unity government and for Jerusalem to be the capital of a Palestinian state in the West Bank and Gaza.
Many Palestinian factions support the plan, but senior Hamas leaders have not yet signed up to it. Hamas, whose charter calls for Israel's destruction, does not recognise Israel, which is implicit in the proposal being put forward.
In the draft government programme posted on Hamas's website in March, the group said it believed the issue of recognising Israel was a matter for the Palestinian people to decide, not merely one faction or another.
National dialogue talks
Abbas gave his ultimatum at a two-day "national dialogue" meeting at which the rival Palestinian factions had pledged to set aside their differences.
The meeting followed weeks of tension between Hamas and the rival Fatah movement since Hamas took office in March. Before Hamas's rise, Fatah was the dominant Palestinian political force.
At the talks, Ismail Haniya, the prime minister and Hamas leader, said: "Our meeting today aims to cement our national unity."
Haniya, who was prevented from addressing the delegates directly in Ramallah in the West Bank because of Israeli travel restrictions, spoke via a videolink from Gaza City.
Members of the Fatah movement
militia take up positions
"I assure our hero prisoners that we will not bring pain into your hearts by having a Palestinian-on-Palestinian struggle... Our difference is with the Israeli occupation and not with any of our brothers," he said.
A power struggle between Haniya and Abbas has led to gunfights between their factions in Gaza in the past week.
Haniya said: "We do not deny that there are differences but we have always stressed that these differences will only be resolved through continued dialogue and in accordance to the law."
Abbas, speaking in Ramallah, said: "We are here because we are at odds ... The danger has reached every house. Our national project is in severe danger.
"Why should we fight each other when we have ... a bigger and greater problem."
Before the meeting, officials in Ramallah said the focus would be on trying to get all sides to adopt a more "pragmatic" position, and said it would also study the financial constraints imposed by Israel and the West since Hamas came to power.
While the dialogue marks an attempt to tackle the power struggle, few expected any breakthroughs.
Hamas officials say they fear the dialogue will be used by some factions to call on the government to step down for failing to run the Palestinian Authority effectively.
Khalil Abu Laila, a Hamas leader in Gaza, said: "If the aim of the dialogue is to show that the government has failed to carry out its duties and must accept a political formula that hints at compromises, then the dialogue will not succeed."