About 250 protesters gathered outside the Pan-Arab TV channel office in Ramallah, and a few sprayed graffiti saying "Al-Jazeera are spies" and "Al-Jazeera equals Israel." A few of the protesters then broke security cameras and windows.
The cache of documents, which detail Israeli-Palestinian contacts over more than a decade, also show Abbas was warned in advance of Israel's 2008 invasion of Gaza.
Abbas today insisted he did not offer secret concessions to Israel.
"What is intended is a mix-up. I saw them present things yesterday as Palestinian, but they were Israeli. ... This is therefore intentional," Abbas told reporters in Cairo after a meeting with Egyptian President Hosni Mubarak.
Hamas, which controls Gaza, quickly launched a sharp attack on Abbas, who heads the moderate Fatah movement.
Hamas spokesman Sami Abu Zuhri said the documents revealed "the ugly face of the Authority, and the level of its cooperation with the [Israeli] occupation."
"These secret documents that were presented by Al-Jazeera are serious," Zuhri said. He added that they show "the level of the Fatah authority's involvement in attempts to liquidate the Palestinian cause, particularly on the issue of Jerusalem and refugees, and its involvement against the resistance in the West Bank and Gaza Strip."
Palestinian officials in the West Bank are concerned that Hamas will try to take over the West Bank as it has Gaza. But Israeli security forces are expected to stop any such attempt, to protect Jewish settlements in the West Bank.
The leaks may cause some dissatisfaction with Abbas, but there does not seem to be any real alternative Palestinian leader. Abbas has repeatedly threatened to resign, and each time has changed his mind.
Another explosive issue concerns the right of return of Palestinian refugees to their homes in what is today Israel. According to the documents, the Palestinians agreed to an Israeli offer to accept 10,000 refugees per year for 10 years, for a total of 100,000 refugees. Presumably, the rest would have the right to return to the future state of Palestine and not to Israel.
If true, this would mark a significant softening of the Palestinian position that all refugees from 1948 and their descendants have the right to return to their homes in Israel. Today that number is an estimated 4 million people. Israeli officials say the right of return means that Israel would not remain a Jewish state.
The documents are based on negotiations carried out in 2008 when former Prime Minister Ehud Olmert was in power. Olmert was forced to resign in 2009 over allegations of corruption and is currently on trial.
Senior Palestinian official Yasser Abed Rabbo, the secretary-general of the Palestine Liberation Organization, also attacked Al-Jazeera.
"In the past they expressed doubts over the views of former Palestinian Authority Chairman Yasser Arafat, just as they do now on the position of Palestinian Authority President Mahmoud Abbas," he said during a press conference in Ramallah. "We did not agree on any proposal regarding East Jerusalem. The only position to which we adhere is Abbas' position that East Jerusalem, according to the 1967 borders, belongs to us."
The leaks clearly damage Abbas, who has tried to pursue peace talks with Israel. Hamas, which controls Gaza, rushed to attack Abbas. A compromise successor to Arafat, Abbas does not have the charisma or the popular support of his predecessor. Abbas has not even visited Gaza, which is supposed to be half of the Palestinian state, since Hamas took over in 2007.
"Abbas is constantly treading the thin line between his will to acquire the sympathy of the Israeli and international public and his need to guard his back from the knives of his rivals at home," wrote columnist Akiva Eldar in the Ha'aretz newspaper today.