The Associated Press has reported that the village headman took the villagers' complaints to the local government, and that local officials have visited the area several times.
However, Phillip Van den Bosche, who runs the foundation, said late Saturday that media reports of friction were "not factual."
He also said that the head of the village "made a very long speech about how grateful he was for this project" at a ceremony for the school.
Raising Malawi is building the school for girls on approximately a 117-acre plot of government land near the capital, Lilongwe. The land had been used by villagers for farming when it was not utilized by the government, but Malawi reclaimed the land when the educational project emerged.
It worked out a deal in which about 200 villagers would be paid 16 million kwacha (about $115,000) in total by Raising Malawi to compensate them for their houses - mostly mud-and-thatch structures - and improvements such as gardens and trees.
Van Den Bosche said the deal - which was worked out by the government but paid for by Raising Malawi - was more than generous.
"If you visited the land prior to this allocation, you would have found that there were at the most one or two small huts" on the land, he said. "The people who were on the land now have an equivalent plot of agricultural land where they can continue their farming ... The community will be enhanced by this."
Last week, government officials met with villagers. One villager, Amos Mkuyu said at the meeting: "My sisters and I inherited this land from our parents whose parents have been here for over a hundred years. How can I get only 200,000 kwacha?"
He received the 200,000 kwacha, or about $1,500, from Raising Malawi for mango trees and three homes on a three-hectare plot. He seems to think the money was also for the land, but the government says the villagers did not have tenure and so are not owed anything for the land. Instead, they have been offered other land.
On Sunday, Van Den Bosche denied that representatives from Raising Malawi had met recently with any villagers about the land issue and believes that others, such as the media and perhaps lawyers, have tried to inflame the issue.
"It was a done deal but of course whenever Madonna's name is involved, opportunism is involved," he said.
"The thought that Madonna would be going on this land to take something away or to hurt people or to bulldoze people out of their homes is ridiculous," he added. "The school is built to build cultural pride, not to destroy it."
Madonna has pumped millions into this impoverished southern African country and become very active in charitable efforts; she has also adopted two children from Malawi.
But while Raising Malawi was co-founded by Madonna, Van Den Bosche said the idea that it was Madonna's school was not accurate.
"Madonna is a donor to this project she's just one of many donors to it, and she has taken the creation of the girls academy on as a pet project of hers, it's something she feels very connected to," he said. "(But) it's not really her school, it's a collaboration."
Van Den Bosche took pains to note that the government has been actively involved in creating the girls school, and that it will be run by Malawians for Malawi's most destitute children. He said 80 percent of girls who finish primary school are not able to go to secondary school, something Raising Malawi wants to change.
The school is targeted to open in 2012, and he hopes it will become a model to educate girls not only in Malawi but in other parts of Africa and the rest of the world where girls receive inferior education.
"We believe it's a beautiful project and we have the support of the village," Van Den Bosche said.
