He said there was no option but for the reconciliation process to succeed.
"We have no choice but to succeed and to move forward dramatically on the road to end division... You are responsible for your people," he told the delegates.
Solving Fatah-Hamas differences is seen also as an essential step if an Israeli-Palestinian peace deal is to happen - although with Israel also at a political crossroads analysts say that could be a long way off.
The Palestinian negotiating committees will next meet on 8 March to continue their work.
About a dozen Palestinian groups are taking part in the national dialogue.
The idea is to form an interim unity government that would prepare for new presidential and legislative elections and co-ordinate the rebuilding of Gaza.
The US, Britain and the EU have made clear that they would rather see non-partisan technocrats in control of the Palestinian territories than a coalition which includes Hamas.
Hamas is accused of using violence to stifle opposition in Gaza
Egypt is hosting an international reconstruction conference on 2 March at which the Palestinians hope to raise $2.8bn (£1.95bn).
A previous unity agreement fell apart after Israel and its international backers refused to deal with Hamas, which refuses to recognise Israel.
Inter-factional fighting in Gaza came to a head in the summer of 2007 when Hamas fighters ousted the pro-Fatah security forces and overthrew PA control.
As well as continued tension, both sides have been accused of conducting politically motivated arrests and the torture of rival faction members.
Egypt revived the call for Palestinian reconciliation talks in November.
However, Hamas withdrew from the talks, complaining that Fatah continued to arrest Hamas members in the West Bank.
Efforts to secure a reconciliation have gained strength since Israel's three-week military offensive in Gaza which ended on 18 January.
The Fatah and Hamas sides have fundamental differences over how to deal with Israel. While Fatah has renounced violence, Hamas refuses to recognise Israel. Hamas is prepared to accept a short-term truce but it reserves the right to fight Israel.
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