The move was made upon the recommendation of the Anti-Corruption Bureau (ACU) which reportedly discovered that some "unusual withdrawals" had been made from the accounts in question since investigations began about the former president and his wife.
Peter Mutharika had lost a presidential election rerun to his current successor Lazarus Chakwera who had promised to stamp out corruption in government.
The former president is being investigated over allegedly shady importation of cement worth 5 billion Kwacha.
One of the frozen accounts belonged to him while another was jointly owned with Gertrude.
As a sitting president of Malawi Mutharika is suspected to have "inappropriately used" his duty-free status to facilitate the importation of the cement consignment without recourse to due diligence, ACU officials said.
Norman Chisale, a former top aide of Mr. Mutharika and Roza Mbilizi, an ex deputy Director General of the Malawi Revenue Authority are of interest tot he ACU over the same issue.