Abbas was re-elected by consensus, party spokesman Mahmud Abu al-Hija said, and was due to address the congress at 6:00 pm (1600 GMT). Some 1,400 delegates were attending.
The election of members of Fatah's parliament and its central committee over the five-day conference will signal the direction the oldest Palestinian party will take at a time when Abbas is weakened by his own unpopularity and internal dissent.
While the ageing leader has said he has no intention of stepping aside anytime soon, talk of who will eventually succeed him as Palestinian president has intensified. He has not publicly designated a successor.
Observers have seen the reduced number of officials to vote -- down from more than 2,000 in 2009 -- as part of a move to exclude Dahlan supporters.
Dimitri Diliani, elected to Fatah's revolutionary council, or parliament, in 2009, said he was not invited to the congress like dozens of others because "we bring a different voice."
He said a press conference set for a refugee camp near Ramallah today with those recently dismissed from the party had been called off after threats "from the security services," including death threats.
Rajoub also said the gathering will provide an opportunity to update the party's structures.
"The system from the 1960s no longer works in 2016," he told AFP.
"We have to take into account the current circumstances. The current system was created when we were in the diaspora and we are now on national soil. It was put in place at a revolutionary stage. Now we have a state."
But the congress also comes at a difficult time for the push to create a Palestinian state, with the cause overshadowed by other crises in the region.
The incoming Donald Trump administration in the US has signalled its policies will be far more favourable to Israel.
Peace efforts have been at a standstill since a US-led initiative collapsed in April 2014.
Fatah is the main component of the PLO, created in 1964 in Jerusalem, which brought together the main Palestinian nationalist movements of that time.
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