She was unaware of the harshly-critical statement that was issued by her office following Madonna's recent visit to the country, senior officials have said.
The statement accused Madonna of exaggerating her contribution to the country and demanding VIP treatment.
Madonna, who was visiting her charity in Malawi, hit back at the criticisms.
She described them as lies and said she began her involvement in Malawi seven years ago 'with honourable intentions'.
A well-placed source told the BBC that President Banda was 'incandescent with anger' when she heard about the statement, and a senior official has confirmed she knew nothing about it.
The statement, issued on Wednesday, accused the star of wanting Malawi 'to be forever chained to the obligation of gratitude'.
It claimed Madonna believed the government should have 'rolled out a red carpet and blast the 21-gun salute' upon her arrival in Malawi.
'Granted, Madonna is a famed international musician. But that does not impose an injunction of obligation on any government...to give her state treatment. Such treatment, even if she deserved it, is discretionary not obligatory,' the statement said.
And, in reference to a row over whether she is building schools or classrooms, it said she 'needs to learn as a matter of urgency...the decency of telling the truth'.
Emily Banda, head of Malawi's NGO board, said that although President Banda 'did not approve' or indeed know about the statement, there would be no apology for the mistake.
Some of the criticism of Madonna's charity work was justified, she said.
Madonna, who has adopted two children from Malawi, originally planned to build an $15m (£9.9m) girls' academy.
But two years ago she closed down the Malawian office of her charity Raising Malawi, which was headed by President Joyce Banda's sister, Anjimile Mtila-Oponyo - who now works at the education ministry - and opted to fund 10 schools instead.
Earlier this month, Malawi's education minister Eunice Kazembe said Madonna was building classrooms, not entire schools, in the country.
'She has built classrooms at existing schools...really it's a difference in terminology,' the minister said.
Trevor Neilson, who is now managing Raising Malawi projects, said $400,000 had been spent on building the 10 school blocks allowing some 4,000 children, who had been learning under trees, to be taught in classrooms.
On Thursday, Raising Malawi put out a statement saying that Madonna 'did not ever ask or demand special treatment at the airport or elsewhere' during her visit.
She said she saw 'with my own eyes the 10 new primary schools in Kasungu province that Raising Malawi...completed this year'.
'Madonna is not letting politics stand in the way of her deep commitment to help build schools there and educate as many children as possible,' the statement also said.
From BBC News