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A spokesman for Madonna has previously said that Malawi's President has a "grudge" after her sister Anjimile Oponyo was sacked as the head of her charitable foundation Raising Malawi.
Ms Oponyo was sacked due to "concerns about mismanagement of $3.8m", said Trevor Neilson, whose Global Philanthropy Group manages Madonna's projects in Malawi.
The allegations have been denied by Ms Oponyo and the President Joyce Banda's office has dismissed the claim.
A statement issued by Madonna's charity Raising Malawi has addressed claims from Malawi's government relating to her behaviour on a recent trip.
Last week, Malawi's President was reportedly angered by Madonna's claim to have built ten schools in the country.
She is quoted as saying: "Where are the 10 schools she has built? She is just building school blocks at already existing schools. In some cases she just renovated an already existing block.
"This is an insult to the people of Malawi. She can't be lying to the world at our expense".
Malawi's government has accused Madonna of demanding special treatment during her recent visit to the country.
The singer - who has adopted two Malawian-born children - recently visited schools her charity helped fund.
A statement issued by President Joyce Banda's office on Wednesday accused Madonna of wanting Malawi "to be forever chained to the obligation of gratitude".
Madonna was also accused of being "a musician who desperately thinks she must generate recognition by bullying state officials instead of playing decent music on the stage".