The Palestine Liberation Organisation (PLO) is facing claims it is no longer relevant as members of the legislative body prepare to vote on members for its executive council.
The Palestinian National Council (PNC) convened in Ramallah in the West Bank on Wednesday to elect six new members to its executive committee.
But the PNC, the highest legal body for Palestinians, is facing criticism from Palestinian factions who say the body has failed to represent the Palestinian people.
Both Hamas and Islamic Jihad have refused to join until the organisation is reformed.
Sami Abu Zuhri, a Hamas spokesperson, told al Jazeera: "The Hamas movement considers the meeting ... illegal because it constitutes a violation of the Cairo and Mecca agreements and the national reconciliation document.
"It contradicts the results of the national dialogue talks in Cairo, in which it was agreed to hold simultaneous elections for the Palestinian National Council and the Palestinian Authority."
Omar Abdul Razzaq, a Hamas parliament member, said his movement would not take part in the meeting, calling it "unauthorised and illegitimate".
Al Jazeera's Nour Odeh, reporting from Ramallah, said the groups' decision was not expected to hurt greater Palestinian reconciliation efforts.
"Many of the members we have been speaking to have pointed out that this should have no bearing on the ongoing efforts to hold national dialogue and reach national reconciliation," she said.
"That is in the hands of these various factions."
Odeh said the groups had agreed in 2005 and again in 2009 to reform the PLO and also to hold elections in January 2010.
"Until that happens, something procedural has to take place and that is elect a third of the executive committee because a third of the positions [became] vacant after six members of the PLO's executive committee passed away," she said.
The meeting comes a day after Salam Fayyad, the Palestinian prime minister, unveiled a plan for building the institutions and infrastructure of an independent state.
The 65-page document calls for a new international airport in the Jordan Valley and rail links to neighbouring states, as well as changes to the economy that would free it from its reliance on Israel.
The Palestinians want an independent state on all the territories occupied by Israel during the 1967 Middle East war, with East Jerusalem as its capital.
But Binyamin Netanyahu, the Israeli prime minister, who is currently visiting the UK, has refused to commit to beginning negotiations on a two-state solution.
Talks between the two sides have been stalled since Israel launched a 22-day offensive in the Gaza Strip last December, which killed at least 1,400 Palestinians.
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