The immediate release of political detainees in Gaza and the West Bank was also promised.
Walid al-Awad, a member of the political bureau of the communist People's Party, said that the committees would begin working on March 10 for, at most, the remainder of the month.
The factions said that they hoped a unity government could reconstruct Gaza after Israel's 23-day offensive which ended last month.
Egyptian mediators said they hoped that a unity deal could be made before an Arab summit is held in Qatar late March.
However, it was unclear what type of cabinet would emerge, with Hamas, who rules the Gaza Strip, differing with Fatah, in the West Bank, on how to deal with Israel.
Amr el-Khaky, Al Jazeera's correspondent in Cairo, said: "What we see today is a real breakthrough regardless of the differences that remain.
"The agreement today on these five committees and that these committees will take decisions unanimously, it wont be a voting system ... and every party will respect it is a breakthrough."
El-Khaky said that Hamas had refused that presidential and legislative elections to be held on the January 20, 2010, because they did not want to give Mahmoud Abbas, the Palestinian president, a mandate.
However, he said that Hamas did agree on the necessity of holding the elections by that date.
"So they are coming nearer to each other, they are compromising," he said.
"And these compromises are painful to both of them after these hostilities and that is why this is the beginning of a breakthrough."
Differences of approach
Hamas so far refuses to renounce violence against Israel, while Fatah favours negotiation.
Marwan Bishara, Al Jazeera's senior political analyst, said: "[The factions] understand very well that for the two billion [dollar] funds to reconstruct Gaza to go in they have to have a national unity government that can receive and spend the money."
Bishara also said that a unity government was also needed for Israel to open the borders and for any legitimate ceasefire to hold.
"So there is a necessity from the outside, Arab pressure to have a party they can deal with, popular Palestinian pressure to have a national unity government once and for all," he said.
Hamas took control of the Gaza Strip from Fatah in a coup in June 2007.