The 54-year-old pop star, who has adopted two children from the impoverished African country, wanted the Malawian government to "roll out a red carpet and blast the 21-gun salute in her honor", according to the statement in the name of President Joyce Banda.
It was "strange and depressing", the statement said, that Madonna appeared to want Malawi's gratitude for her adoption of David and Mercy.
"Kindness, as far as its ordinary meaning is concerned, is free and anonymous. If it can't be free and silent, it is something else. Blackmail is the closest it becomes."
Malawi's State House rejected claims that Mrs Banda had refused to see Madonna because she sacked her sister as head of her charity in the country and rubbished her assertion that she had built 10 schools there, saying she should "learn as a matter of urgency the decency of telling the truth".
"Madonna feels that the Malawi Government and its leadership should have abandoned everything and attended to her because she believes she is a music star turned benefactor who is doing Malawi good," it read.
"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," Tusekele Mwanyongo, a State House press officer, wrote.
Madonna's relationship with Malawi began in 2006 with David's adoption, but soured after a report accused many of the local staff running her Raising Malawi charity of financial impropriety. She returned to Malawi last week to review the progress of her plan to build 10 community schools, and asked for an audience with the president in a hand-written note.
Not only did the visit not take place but there followed a series of angry statements from the Malawian government about the singer's claims to have built schools.
President Banda was quoted as slamming her for "making poor people dance for her".
On Saturday, as she flew home, Madonna reportedly found herself stripped of the VIP status which she was afforded when she arrived in the country, meaning she and her entourage were forced to queue through customs and security in Lilongwe airport's ordinary passenger terminal.
Trevor Neilson, Madonna's spokesman who travelled to Malawi with her and her four children, told The Daily Telegraph last week that President Banda, who has courted foreign donors assiduously since taking office last year, was acting on a grudge against Madonna held by her sister, Anjimile Mtila-Oponyo.
Mrs Oponyo is a Malawian development worker who was picked by Madonna to be CEO of her Raising Malawi charity but sacked after accusations that she stole money - claims that have been denied.
"For her to accuse Mrs Oponyo for indiscretions that have clearly arisen from her personal frustrations that her ego has not been massaged by the state is uncouth, and speaks volumes of a musician who desperately thinks she must generate recognition by bullying state officials instead of playing decent music on the stage," the State House missive read.
It concluded that Madonna was welcome in Malawi as any other philanthropist, noting that among others who had visited without red carpet treatment included Chuck Norris, Bono, David James, Rio Ferdinand and Gary Neville.
"However, acts of kindness must always remain as such; they must not smack of blackmail."
Trevor Neilson, Madonna’s “philanthropic adviser” and spokesman, responded by repeating his claim that Mrs Banda was acting on her sister’s grudge against the singer.
“Madonna is the largest individual philanthropist in Malawi and we are a bit surprised that the president is using her office to pursue her sister’s financial interests,” he said. “That said, we will continue to fund programs that support children in Malawi, a country where millions of children suffer every day.