Nasser said that "some people" from Fatah's leadership in the West Bank had "hijacked" the conference.
Nearly all 18 of the 23 Central Committee seats which were up for election had, according to early results, gone to Fatah delegates from the West Bank.
Only two Fatah delegates from Gaza, Mohammed Dahlan from the central refugee camp of Khan Younis and Nabil Shaath from Gaza City, were confirmed as making it into the party's powerful Central Committee.
Gaza delegates had demanded at least six posts.
They claimed that voting by about 400 Gaza Fatah delegates during a recent party convention had been unfair, inaccurate and chaotic, with some delegates voting more than once.
The group said they were forced to vote in the party election by phone after the Hamas movement, which has de facto control in the Gaza Strip, refused to allow their departure to attend the conference.
Vote counting in the elections for the Revolutionary Council of the party will take at least three days, due to the large number of candidates and problems with the parallel elections to the Central Committee, election officials said on Wednesday.
A total of 617 candidates are contesting the 80 seats up for grabs in the 120-seat council. The remaining 40 seats will be filled by appointment.
The Revolutionary Council plays a legislative role in Fatah's leadership.
Organisers announced later on Wednesday the final results of the Central Committee elections, which showed only minor changes from the unofficial tally.
The result saw a key aide of the Palestinian president unexpectedly enter the movement's top decision-making body.
Presidential Secretary Tayeb Abdul Rahim, a long-time Abbas supporter and a member of the outgoing Fatah Central Committee, was initially believed not to have made it into the newly elected Central Committee.
But Ahmed Sayyad, chairman of the election committee for the party's convention, said some of the ballot boxes had been recounted after protests.
Speaking at the conference hall in the West Bank city of Bethlehem, Sayyad announced the final Central Committee list, which included six members of the outgoing committee.
Nabil Sha'ath and Muhammad Shtayya tied, receiving an equal amount of votes and both coming in as number 18.
With Abbas, that means that 20 of the 23 seats are now filled.
The remainder is to be appointed by the newly elected committee.
Al Jazeera's Nour Odeh reporting from Bethlehem said: "We are hearing that the results will be endorsed - a new Committee with a majority of fresh faces and fresh ideas and probably a new approach of doing business.
"The new members of the committee have pledged not to resume negotiations with Israel until and unless Israel stops all settlement activity, including that in occupied East Jerusalem.
"They've asked the Obama administration to stand firm on this issue and stand with the Palestinian Authority and the Arab world in demanding Israeli compliance.
"This new committee says they will strive to achieve unity with Hamas, but they will not compromise on key issues of policy in order to do that."