As polling stations opened as much as 10 hours late, anger and speculation about the fairness of the vote spilled over into violence -- mirroring the country's volatile politics.
On the outskirts of the commercial capital Blantyre, an AFP reporter saw the smouldering remains of a polling station that had been torched by voters protesting late delivery of balloting material.
A tent used as a polling station was burnt in another Blantyre township, according the electoral commission chief Maxon Mbendera.
"Maybe they are trying to rig the election," said Paul Wind, 38. "If they think they will frustrate us from voting, they are wrong," he added.
Another voter Fanuel Kapenga says "this causes doubt, especially if the ruling party wins."
The stakes are high in this, the first election since hard-line president Bingu wa Mutharika died in office two years ago, with his rival heirs reprising their battle for power.
In the days after his death, Mutharika's body was secretly flown around Africa as his brother Peter allegedly tried to prevent Joyce Banda -- then vice-president -- from being sworn in.
For 74-year-old Peter Mutharika winning would mean an end to his trial for treason.
Analysts predict Banda will win albeit with a slender majority.
"I think the president still has a fighting chance of winning," said Boniface Gulani a political scientist at the University of Malawi.
But with the victor expected to take 40 percent or less of the votes cast in a do-or-die political battle, the potential for further violence is high.
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