Many of the men had been in the compound for months
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Palestinian security forces have arrested about 20 militants inside the West Bank headquarters of Yasser Arafat.
Those detained at the Palestinian leader's Ramallah compound belong to Yasser Arafat's Fatah movement and its armed offshoot, al-Aqsa Martyrs' Brigade.
Many of the men have been inside the compound, which was besieged by Israeli forces twice, for months.
They had not left for fear of being seized by the Israelis who described Saturday's arrests as significant.
The BBC's Damian Grammaticas in Ramallah says he understands the men will be held at a Palestinian jail in Jericho which is under American supervision.
None are thought to be from Hamas or Islamic Jihad - the main Palestinian militant groups that are observing a three-month truce with Israel.
Palestinian leaders, including Prime Minister Mahmoud Abbas, have come under increasing pressure from Israel and the US to crack down on "the infrastructure of terror".
'Bad advice'
Israel says the men are militants wanted for attacks against Israelis.
They were arrested on Saturday morning and are believed to be confined to a room inside the headquarters awaiting the move to Jericho.
Israel has often said it may deport Arafat
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Kamel Ghanam, Ramallah chief of the al-Aqsa Martyrs' Brigades, said the militants had been arrested after refusing Yasser Arafat's request to be transferred to Jericho, according to the Associated Press news agency.
Mr Arafat had asked the men to move because "the world has changed", Mr Ghanam said.
The al-Aqsa official said the militants would resist attempts by Palestinian security forces to remove them.
Dismay?
The militants sought refuge inside the Muqata headquarters which was largely reduced to ruins in two Israeli assaults last year.
Their arrest appears to be a compromise - the men, will, after all be held in a Palestinian, not Israeli jail, our correspondent says.
But there will be dismay among some Palestinians at the actions of their police, he adds.
In a statement following the arrests, al-Aqsa vowed to resume attacks - "in particular suicide operations" - to avenge the "Americo-Zionist decision to arrest the activists".
The group has been behind a number of attacks since 29 June, when the main militant groups signed a truce.
Prime Minister Mahmoud Abbas - also known as Abu Mazen - has come under pressure to take action to comply with the internationally-backed peace plan - the "roadmap".
Abu Mazen is the US and Israel's chief interlocutor - the two countries refuse to deal with Mr Arafat, accusing him of supporting attacks on Israelis.
The veteran Palestinian leader has been confined to his headquarters for most of the time since the current intifada began in September 2000.