Charles Mataya the associate professor, confirmed his decision, cited management sidelining of the board in borrowing the controversial K30 billion from commercial banks as the main reason.
The Malawi Revenue Authority (MRA) borrowed the money to paint a rosy picture of revenue collection for the hastily implemented zero-deficit budget (ZDB) to show that it was on track.
Mataya said management did not consult the board on the borrowing and he felt like it (the board) was reduced to a mere rubber-stamp.
Said Mataya: “I resigned today and I do not know who is acting because that is not part of the agenda.”
Mataya has been replaced by financial guru Thom Mpinganjira.
Mataya`s decision also comes amid calls for the resignation of Finance Minister Dr Ken Lipenga and MRA Commissioner General Lloyd Muhara to pave way for investigations to ascertain the extent to which the Democratic Progressive Party (DPP) administration went to mask the state of the country`s economic collapse.
Mataya said the board was shocked by Lipenga`s revelations that MRA borrowed the money from banks to portray ZDB as a success story.
“We never authorised that borrowing. We were never made aware of it,said Mataya.
Lipenga`s admission of the borrowing on Tuesday last week raised resignation calls from various quarters who accused him of feigning ignorance.
Commentators were irked further after Lipenga claimed his hands were clean on the transaction, arguing he did not sanction MRA to borrow from commercial banks to beef up its performance.
He said the report he presented in Parliament in February was based on information given to him by his officials and claimed he did not have any reason to suspect there were discrepancies.
Experts counter-argued that lying to Parliament and the nation was not a simple thing.
They said Lipenga should not pretend to be ignorant of the transactions as MRA would only get such a mandate from his ministry.
They further said for MRA to borrow, Parliament has to pass a loan authorisation bill.
The scam was first brought to light in February this year by Malawi Forum for Unity and Development (Mafunde) president George Nnensa who claimed he had evidence that MRA borrowed the money from the Malawi Savings Bank (MSB), NBS Bank Limited, Standard Bank, National Bank of Malawi and Indebank Limited at the end of December 2011.
Nnensa, who is Balaka South MP, reported the money was repaid in January this year with interest.
Meanwhile, Lipenga, said he has submitted a report on the matter to President Joyce Banda.
He said he is ready to resign if he is implicated.
Traditionally, donors support the country`s national budget with resources estimated at 40 percent.
