It comes after a Malawian government spokesperson told news outlets the 58-year-old singer had appeared in court and had "filed an application expressing interest" to adopt.
Madonna is currently in the African country, but said her visit was strictly for charity purposes.
"The rumours of an adoption process are untrue," she said in a statement.
"I am in Malawi to check on the children's hospital in Blantyre and my other work with Raising Malawi and then heading home."
Court spokesman Mlenga Mvula had told news agencies earlier on Wednesday the singer had appeared in High Court, applying to adopt two children.
"As a court, we adjourned the matter for a ruling (in the next two weeks). The court will either grant the adoption order or might not," he said.
Madonna previously adopted two children from the African country: David Banda in 2006 and Mercy James in 2009.
The star's relationship with Malawi dates back to 2006, when she established the Raising Malawi charity, with the goal of improving children's lives.
She initially planned to build a $15m (£12m) girls' academy, but later changed strategy, and used the money to fund a number of schools.
The charity also provides scholarships to female students, and is currently building the country's first paediatric intensive care unit at the Queen Elizabeth Central Hospital, in Blantyre.
Madonna visited the project last summer, and took David and Mercy to visit the orphanages where they lived before being adopted.
The star has two other children - Lourdes and Rocco - from previous relationships. Last year saw her involved in a custody dispute over Rocco with ex-husband Guy Ritchie.
She eventually lost the case, with the 16-year-old moving to London to live with his father.