The pop star landed in the capital Lilongwe at around 11am on Wednesday, accompanied by David Banda and Mercy Chifundo, two children she adopted from the country, and her 14-year-old son Rocco along with an entourage that included advisers and bodyguards.
On Friday, Madonna is due to meet Malawi's new president Peter Mutharika, who took over from Joyce Banda at the last elections.
Madonna and Mrs Banda had a series of public disagreements after the pop star sacked her sister, Anjimile Mtila-Oponyo, as head of her Raising Malawi charity.
Madonna tried to meet Mrs Banda during a visit to Malawi last year, but the president said the star was simply trying to get 'poor people to dance for her' and refused, also accusing her of 'blackmail' and 'bullying'.
She then stripped the Material Girl singer of her VVIP status, forcing her to check into her private jet at Kamuzu International Airport as an ordinary passenger.
On Wednesday, Madonna was restored to VVIP status.
'We were asked to clear the airport's cargo bay for a special guest,' said an airport official.
He said Madonna was whisked into a fleet of SUVs and driven into town to Kumbali Lodge, a farm lodge where she always stays on her visits to Malawi.
The American star is due to hold talks with Mr Mutharika on Friday at his official resident, the Kamuzu Palace.
'We welcome Madonna as guest of the government and people of Malawi,' said State House Press Secretary Frederick Ndala. 'The President appreciates the charity work she is doing for the people of Malawi.'
Trevor Neilson, president of the Global Philanthropy Group which works with Madonna, said her charitable endeavours in Malawi have included building schools for over 1,000 students and funding clinics and orphanages.
From Daily Telegraph