He was originally scheduled to attend the Anti-Corruption Bureau on Tuesday to answer questions on alleged fraud and tax abuses, but Mutharika excused himself.
Instead, the 81-year-old politician issued an angry statement saying he would exercise his right to “remain silent”.
After the bureau rescheduled the interview to Wednesday morning, Mutharika excused himself on health grounds.
“He was taken ill and he went to see (his) doctor,” the agency’s spokeswoman Egrita Mdala told AFP.
The bureau last week said they wanted Mutharika to answer questions over the alleged abuse of his taxpayer identification number.
He has been accused of having used it while he was still in office to import millions of dollars worth of cement free of duty, which was then sold at commercial rates.
In his statement Tuesday, Mutharika said the inquiry was “continued persecution and harassment” and was “intended to humiliate and taunt me psychologically”.
A year ago Mutharika, then the incumbent, lost a presidential re-election ordered after a top court annulled his victory over electoral irregularities.
His successor, President Lazarus Chakwera, campaigned on a platform of fighting corruption.