Al Jazeera's Nour Odeh in the West Bank, said: "The talks have not failed. Palestinian leaders are still closer than ever to a unity deal."
No clear agreement
Senior members from the Palestinian factions said on Thursday there was still no clear agreement on key issues, namely how to approach existing agreements with Israel.
Other sticking points remain the programme of a government and its composition, the leadership of the security apparatus, and the reformation of the Palestinian Liberation Organisation (PLO), Odeh said.
Negotiations have reportedly turned away from discussing a government of national unity and instead have been based on the formation of a government of "consensus".
However, sources from Hamas said the talks ended in a very positive mood, and that they were committed to reaching a comprehensive agreement.
Fatah sources said that some Fatah and Hamas leaders would stay in Cairo, while others would return to the West Bank and Gaza.
Fawzi Barhoum, a Hamas spokesman, issued a statement to reporters on Thursday in Cairo saying Hamas-allied groups and Fatah had agreed on forming a government "whose specific job will be to hold elections before the end of the year".
Reports from the meeting suggested there had been agreement on the holding of elections in January 2010.
Earlier on Thursday, Egypt's official Mena news agency quoted the leader of the Palestine Liberation Front (PLF) as saying any unity government would be transitional in nature.
Hamas and Fatah faction of Mahmoud Abbas, the Palestinian president, have been bitterly divided since Hamas, after winning a majority in a 2006 parliament election, seized Gaza in a week of deadly fighting in June 2007, limiting Abbas's authority to the West Bank.