Relations between the rivals have worsened in recent months
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Palestinian President Mahmoud Abbas and PM Ismail Haniya have agreed to urge armed men from their rival Fatah and Hamas factions to leave Gaza's streets.
Mr Haniya said they would appeal for calm and a return to negotiations on forming a government of national unity.
The meeting between the two men, the first in two months, followed renewed factional bloodshed in northern Gaza.
Meanwhile, Israeli troops carried out further raids in the West Bank, a day a after deadly incursion into Ramallah.
Reports said troops had entered the village of Attil, near Tulkarm, and detained two militants.
In the city of Nablus, Israeli troops clashed with Palestinian gunmen. Palestinian sources said three members of the al-Aqsa Martyrs Brigades militant group had been injured.
Inquiry ordered
Mr Haniya cut short a trip abroad to meet Mr Abbas in Gaza City.
"We have decided to appeal for calm and for the withdrawal of all the armed men from the streets, and to continue the dialogue," he told journalists after the meeting.
Mr Haniya added that he had decided to set up an inquiry into the recent inter-Palestinian clashes.
Mr Abbas did not make a public statement after the talks.
Separately, Reuters news agency reported that the US administration was planning to provide security forces loyal to Mr Abbas with $86.4m.
The agency quoted a US government document saying that the money would "assist the Palestinian Authority presidency in fulfilling PA commitments... to dismantle the infrastructure of terrorism and establish law and order".
Dramatic killing
The Abbas-Haniya meeting took place after a very senior figure in a security service linked to Fatah, Col Mohammed Ghayeb, was killed when gunmen attacked his home, Fatah officials said.
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They are targeting the house. For God's sake, send an ambulance
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Four of his bodyguards also died, and his wife was wounded.
The BBC's Alan Johnston in Gaza says there are reports the Hamas men may have blamed the bodyguards for the death of one of their comrades in an earlier clash.
Col Ghayeb was heard pleading for help in a phone call broadcast by Palestine TV, Associated Press reported.
"They are killers. They are targeting the house, children... are bleeding. For God's sake, send an ambulance, we want an ambulance, somebody move," he was heard saying.
A member of a security force set up by Hamas was also shot dead in the Jabaliya refugee camp in northern Gaza.
On Wednesday, five people died in factional fighting, including a 21-year-old woman who was hit by a stray bullet.
Relations between the two parties have always been bad, our correspondent says, but they have worsened significantly in recent months as political differences have deepened.
Fatah advocates negotiations to found a state alongside Israel while Hamas refuses to recognise Israel's right to exist.