Madonna, who adopted two children from the country, has helped build several schools through her Raising Malawi charity.
The BBC said the singer recently complained to Malawi officials she was poorly treated during a visit to the country.
However, the government countered she is exaggerating her contributions to Malawi and demanding special treatment, such as skipping lines for passengers at the airport and not being frisked by security officials.
"Granted, Madonna is a famed international musician. But that does not impose an injunction of obligation on any government under whose territory Madonna finds herself, including Malawi, to give her state treatment. Such treatment, even if she deserved it, is discretionary not obligatory," a statement issued Wednesday by Banda's office said.
"Among the many things that Madonna needs to learn as a matter of urgency is the decency of telling the truth," the statement said. "For her to tell the whole world that she is building schools in Malawi when she has actually only contributed to the construction of classrooms is not compatible with manners of someone who thinks she deserves to be revered with state grandeur."
"Madonna is the largest individual philanthropist in Malawi. We will continue to fund programs that support children in Malawi," Trevor Neilson, Madonna's manager, told the BBC.
Neilson also accused the government of financial mismanagement of school project funds and of "harassing organizations that Raising Malawi has donated to."