Palestinian security services have been destroying secret files, fearing Israeli raids on their offices as the Jewish state weighs annexing parts of the occupied West Bank, sources in such organs say.

"We have been ordered to destroy confidential documents in our possession and we have obeyed this order," a Palestinian security source told AFP on condition of anonymity, saying that the instructions came from "high up".

During the Palestinian uprising known as the Second Intifada, which erupted in the early 2000s and included waves of suicide bombings, Israeli security forces repeatedly stormed Palestinian security services' offices and removed confidential documents.

Several Palestinian security sources, speaking on condition of anonymity, said the services are concerned that this could happen again if Israel moves ahead with annexation.

US President Donald Trump's Middle East peace plan, unveiled in late January, envisions Israel annexing its settlements and the Jordan Valley in the West Bank.

More than 450,000 Israelis live in settlements deemed illegal under international law, alongside 2.7 million Palestinians in the wider West Bank.

Washington's proposals provide for the creation of a Palestinian state, but on reduced territory and without Palestinians' core demand of a capital in east Jerusalem. The plan has been rejected in its entirety by the Palestinians.

One Palestinian security source, who did not describe the nature of the documents, said the security services began destroying them a month ago, around the time Palestinian president Mahmud Abbas said he was ending security coordination with Israel.

Two other security sources said some documents were destroyed after they were scanned and transferred to USB drives, which were then put in "secret places".

According to the 1993 Oslo Accords, the Palestinian Authority controls all Palestinian cities in the West Bank, but the Israeli military can enter them to make arrests, in coordination with local authorities.

But in May, Abbas declared that he no longer felt bound by the treaties, saying that Israel's annexation plans showed that it was no longer honouring the agreements.

Analysts said the end of security cooperation could inflame unrest in the West Bank.

Palestinian security forces man a checkpoint at a key entrance to the city of Hebron earlier this year
Palestinian security forces man a checkpoint at a key entrance to the city of Hebron earlier this year AFP / HAZEM BADER

Palestinian prime minister Mohammed Shtayyeh recently warned of a "hot summer" if Israel goes ahead with its annexation plan.

Palestinian authorities accused Israel Tuesday of an incursion into Ramallah, the West Bank seat of the Palestinian Authority, for the first time since the end of security cooperation.

Israeli forces "searched three houses inside Ramallah, but did not make any arrests," Ghassan Nimr, spokesman for the Palestinian interior ministry, told AFP.

According to a security source, a 20-year-old Palestinian man was arrested in the Al-Amari refugee camp, which borders Ramallah.

The source reported clashes between stone-throwing youths and Israeli soldiers who responded with tear gas, but said nobody was wounded.

Questioned by AFP, the Israeli army confirmed having made an arrest in Al-Amari, but denied entering the city of Ramallah itself.

The Palestinians have so far staged two Intifadas against Israeli rule, the first in 1987.

A recent poll showed that a majority of Israelis fear a third uprising if annexation goes ahead.

Shtayyeh said the Palestinian Authority, led by president Mahmud Abbas, wanted to avoid widespread disruption.

But, "the anger is there, the dissatisfaction is there, the frustration is there," he said.