Banda said the vote has seen ballot tampering, presiding officers arrested, people voting multiple times and the collapse of the computerised voter counting system.
"It has come to my attention that there (are) some serious irregularities in the counting and announcement of results in some parts of the country," she said calling for an "immediate manual audit of the whole process".
This is the first major electoral test for the 64-year-old former vice-president, who came to power when president Bingu wa Mutharika died in office two years ago.
But her government has since been ensnared in a USD 30 million government corruption scandal dubbed "Cashgate" that has seen foreign donors freeze badly needed aid.
Amid unconfirmed reports that Banda is trailing in the polls to Peter Mutharika, the former president's brother, she warned the media against "creating a false impression of the possible winners".
Earlier today a junior minister in Banda's government Godfrey Kamanya committed suicide, apparently because of the election result.
Voting had been scheduled to take place on Tuesday, but was extended through to today when delays of up to ten hours prompted riots in the commercial capital Blantyre, where the army was deployed.
But Banda's request for an audit was rebuffed by the country's electoral commission chief, who told AFP that despite problems with the electronic counting system, the tally was continuing manually.
Maxon Mbendera insisted the election was "valid" and said Banda's claim was caused by "desperation".
Election observers from the European Union have described "considerable organisational shortcomings" in the vote and "isolated incidents of unrest".
They have so far not given a verdict on the fairness of the poll, but said the election commission had "acted impartially throughout".