The minister, Brown Mpinganijira, told the state radio that Banda has been receiving death threats some of which came from outside the country.
“The President has been receiving death threats, some of the threats have come from outside the country,” Mpinganjira told state radio.
He said police is investigating the threats.
Banda on October 10 dissolved her cabinet over a graft scandal where top official are suspected of stealing more than $3 million from state coffers.
A few weeks ago, a budget director in the ministry of finance, Paul Mphwiyo, who had been investigating a fraud ring amounting to millions of dollars from the state, was shot outside his home.
“It all shows how serious the battle against fraud and corruption is,” Mpinganjira said.
Banda, who is the country’s first female president, came to power in 2012 after the death of Bingu wa Mutharika.
Prosecutors estimate that as much as one-third of the country’s revenue is lost to fraud and graft-linked pay-outs, while about 40 per cent of Malawi’s national budget comes from aid.
The EU has threatened to suspend aid to Malawi after the scandal and Norway has also halted funds.