Fatah officials said in a statement that the votes cast on Monday would be nullified and the primary would have to be rescheduled.
"The Fatah General Committee held an urgent meeting in Gaza this afternoon to evaluate the primary elections, and the committee decided to freeze the election due to the serious violations that took place during the voting process today," the statement said.
The Gaza primaries were expected to continue the trend from earlier voting in several West Bank districts that swept away many of the entrenched old-timers, who controlled the party for decades and were seen as corrupt, and replaced them with young politicians more popular with average Palestinians.
The housecleaning in Fatah is crucial to the party's hope of beating back a strong showing by the Palestinian resistance movement, Hamas, which has wooed Palestinians in part with its image as an honest group that will not tolerate corruption and bribery.
Parliamentary elections are set for 25 January, and Fatah spokesman Diab Alluh said new lists of candidates would have to be presented by 3 December.
A Fatah member votes in the Gaza
Strip on Monday
After the primary, Abbas will review the results and choose the candidates.
Change in leadership
Before the cancellation, Muhammad Dahlan, a Palestinian Authority official who is seen as a bridge between the two generations in Fatah, was greeted by scores of chanting supporters as he voted in a sports club in the refugee camp of Khan Yunus in the central Gaza Strip, where he is running for a space on the ballot.
"The election has brought a clear and obvious answer that the leadership has to be changed," said Dahlan, who grew up in the camp. "We need an internal, positive revolution within Fatah that can guarantee the dignity of our old-timers - our leaders - and the continuation of Fatah."
Even before the new problems emerged, scheduled votes in Rafah and areas of central Gaza were postponed until Wednesday because of technical hitches, Fatah officials said.
In one station in a village in eastern Khan Yunus, a group of about 15 armed men came to vote. When they did not find their names on the registration list, they fired in the air, witnesses said.
"We respect the old generation, but it's time to give us a chance. The world is changing and so are we"
Majdi Abu Daka,
Officials closed the polling station for about 45 minutes after the incident.
A similar incident in the northern Gaza town of Bait Hanun forced the closing of a polling station there, officials said.
Several voters at the sports centre in Khan Yunus welcomed the primary for giving a voice to grass-roots party members and allowing younger activists a chance to break into Fatah's higher ranks.
"We want new blood in Fatah's body. We want to say that Fatah is able to lead and to bring us our rights," said Majdi Abu Daka, a 34-year-old engineer. "We respect the old generation, but it's time to give us a chance. The world is changing and so are we."
Many of the veteran Fatah leaders had lived in exile for decades before moving to the West Bank and Gaza in the 1990s - after the signing of interim peace accords with Israel - and securing powerful positions with the Palestinian Authority.
Armed men fired in the air at
several Gaza polling stations
Members of the "young guard" spent their lives in the Palestinian territories, cut their teeth as leaders of the first Palestinian uprising in the 1980s and spent time in Israeli jails, giving them credibility with younger Palestinians.
The biggest winner in the primaries last week was Marwan al-Barghuthi, a charismatic Fatah leader who is serving five consecutive life sentences in an Israeli jail for his alleged involvement in the killing of four Israelis.