Two polling centers were set ablaze in the eastern city of Benghazi, said Alexander Graf Lambsdorff, head of the EU election assessment mission. And in two other cities, polls did not open until 2 p.m. (six hours before they were set to close).
In the eastern city of Ajdabiya, five polling centers opened but four others on the outskirts did not.
On Friday, anti-aircraft fire hit a Libyan air force helicopter transporting ballot boxes from the eastern city of Benghazi to nearby areas, the Interior Ministry said. One person was killed. It was unclear who was behind the attack.
And protesters earlier this week attacked a warehouse and torched ballots and other election materials.
This was one of several anti-election incidents staged by Libyans in the east who see an unequal distribution of seats in the national assembly. The 200 seats are allocated by population, reserving 100 for the western Tripolitania, 60 for Cyrenaica in the east, and 40 for the south.
The mistrust stems from the many years of Gadhafi's rule, under which the eastern region felt largely neglected and marginalized. Benghazi emerged as the cradle of the Libyan uprising but many of its residents now feel their revolution has been usurped by the National Transitional Council based in Tripoli.
Mohammed al-Sayeh, a member of the National Transitional Council, dismissed the disruptions as "minor" and said there was no lack of trust between east and west.
"Libya will be always united," he said. "It is the first fair and legitimate election."
Authorities flew in fresh ballots printed in the United Arab Emirates, but the shipment did not arrive in time for all the Ajdabiya polls to open.
Seven other polling stations in and around Benghazi were also closed due to pro-federalist threats against voters.
As the polls came to a close Saturday evening, Lambsdorff said it was too early to tell whether the election had been compromised by the violence.
"Again, we are talking about single isolated incidents," Lambsdorff said.
Saturday's vote is sure to be a litmus test for post-Gadhafi Libya. The new national assembly will be tasked with appointing a transitional government and crafting a constitution.
The nation's new leaders, however, will have their work cut out for them as they begin a new, more democratic era.
Amnesty International published a scathing report this week about what it described as lawlessness in Libya, with the advocacy group urging the nation's authorities to establish a functioning judiciary and rein in revolutionary militias that are accused of committing a plethora of human rights violations.
The disparate groups came together to topple Gadhafi but remain divided along regional lines. More than 200,000 Libyans are still armed and often operate outside of the law, according to Amnesty.
Security is just one of many obstacles.
The new government must figure out how to unify the country as it moves forward. That includes a reconciliation process for Gadhafi loyalists.
And there is the task of rebuilding a nation ravaged by dictatorship and last year's conflict.
The National Transitional Council, Libya's de facto rulers since Gadhafi was captured and killed in October, inherited a land where few civil institutions existed. The new government will have to create a functioning society out of that vacuum.