A delegation of the Ecowas observer mission monitor the counting of cast votes at a polling station in Bamako.
A low turnout and vote abuses marred Sunday elections meant to complete the democratic transition in Mali, after a coup last year led to an Islamist takeover of the north that was crushed by French military intervention.
Officials said armed men carried off ballot boxes from some bureaux in the Timbuktu region of northern Mali, preventing some people from casting their votes in the legislative poll.
It was not immediately clear who was responsible.
The west African country has suffered a surge in Islamist violence since President Ibrahim Boubacar Keita was elected in August in a vote that marked a return to democracy after the March 2012 coup.
The military putsch plunged Mali into chaos and allowed al-Qaeda-linked fighters to seize the northern two-thirds of the country.
France launched a massive military operation in January that drove the Islamists from northern towns, but isolated cells have remained active.
Vote counting began after some 25 000 bureaux across the country closed at 6pm (GMT).
Few ballots
Only a fraction of the 6.7-million people registered to vote appeared to have cast their ballot and there was no sign of the long queues of voters that marked the presidential vote.
"Compared to the presidential elections the turnout was very weak. In my bureau, we didn't even get a third of the voters," said Oumar Samake, president of a voting bureau in Bamako.
"Political parties have to do more to inform their voters."
Malian soldiers, French troops and UN peacekeepers protected voting station in the north following the resurgence of Islamist violence.
Gao, the largest city in northern Mali, was targeted in a rocket attack on Thursday by suspected Islamists.
The election of a new parliament is supposed to complete the democratic transition in the wake of last year's coup.
Donors have pledged $3.25-billion to rebuild the impoverished country and develop its lawless desert north.
Despite some discontent in southern Mali with his peace overtures to northern Tuareg separatist rebels, Keita's RPM party is expected to comfortably win the election.
Universally known by his initials IBK, Keita swept the August 11 presidential runoff with 78% of the vote.
"The aim of my vote is to give a comfortable majority to the president and his allies," said Boubacar Ouedrago, a butcher in Bamako.
"IBK needs this majority to complete his mission."
Protest in Kidal, gunmen in Goundam
Some 1 087 candidates from 410 electoral lists competed for the 147 seats in Parliament.
A second round will be held on December 15 in constituencies where there is no majority winner.
Keita's losing presidential rival, Soumaila Cisse, aims to secure the post of parliamentary speaker and has pledged to form a vocal opposition, according to sources close to him.
The unity governments of former president Amadou Toumani Toure, which curtailed debate and accountability, have been blamed for damaging faith in Mali's political system, encouraging the 2012 coup.
Keita's RPM party was the only one on the electoral list in the far north region of Kidal, where it has enlisted the support of some of the leaders of last year's uprising.
Opposition candidates say it has been too dangerous to campaign there.
About 100 supporters of separatist parties staged a march in Kidal's dusty centre to protest against the elections but were prevented from entering voting stations by members of the UN peacekeeping mission, residents said.
Oumou Sall Seck, mayor of the town of Goundam about 65km from the ancient caravan town of Timbuktu, said voting was impossible in five of its communes due to the disappearance of electoral materials or the theft of ballot boxes by armed men.
"They were militia. They were armed and well-organised, moving around on vehicles," said Seck, a member of Cisse's opposition URD party.
Officials also reported gunmen taking materials near Lere, 160km southeast of Timbuktu.
France has more than 2 000 troops stationed in Mali but aims to reduce its military presence to 1 000 by February as it hands security responsibilities to the Malian army and the UN force.
The UN mission, launched in July, is still at roughly half its 12 600 planned strength. – Reuters