The official who could not be named because he was not authorized to speak on the matter said Madonna arrived at about 8:30 a.m. ET Sunday on Ethiopian Airlines.
The 51-year-old celebrity was accompanied by her four children - Lourdes, 13, Rocco, 9, as well as her two adopted children. Madonna adopted the Malawian-born Mercy, 3, this year and David, 4, in 2008.
The official said Madonna would take part in a groundbreaking ceremony for the school on Monday.
Madonna's Raising Malawi, a charity founded in 2006 when she first visited the country, helps feed, educate and provide medical care for some of Malawi's orphans.
Malawi, a nation of 12 million, is one of the poorest countries in the world. About 500,000 children have lost a parent to AIDS.
Madonna will also meet with President Bingu wa Mutharika and visit some of the orphanages her charity supports.
The school she is building for poor girls is on the outskirts of the capital and is similar to the one built by talk show host Oprah Winfrey in South Africa.