The system "is refusing to take the information from the ground where our data clerks are stationed to send the results," chief elections officer Willie Kalonga told AFP two days after the vote.
As a "back-up solution," officials in the southern African country's 28 districts were sending the results manually via fax and email to the national elections centre in Blantyre.
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The military was deployed to restore calm after irate voters set alight poll stations in protest at them opening up to 10 hours late, with election materials unavailable in places.
Voting spilled into an unscheduled second day, yesterday at 13 voting stations, and thousands queued to cast their ballot.
Commonwealth observers noted "serious shortcomings" in the distribution of ballot papers, boxes, forms, ink and lamps for voting after dark.
"A considerable number of polling stations opened late on account of these shortcomings," it said in an interim report today.
But the Commonwealth deemed the vote "peaceful, orderly and transparent" overall, despite "isolated incidents of violence" owing to frustration with the delays.
"The polling environment was generally conducive to the free expression of will by the electorate," it concluded.
Around 7.5 million people were eligible to vote in the fifth democratic elections since the end of dictatorship 20 years ago.
The MEC will only announce results when 30 per cent of the votes have been counted, and is currently "not anywhere in the neighbourhood" of that figure, MEC chairman Maxon Mbendera said yesterday.
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