The superstar, who adopted two children from the southern African nation, has been involved in a long-running spat with Malawi's government over her charity work in the country.
In a statement posted on the website of her charity Raising Malawi, Madonna accused the government of corruption and of failing its people.
"I am so sad to see that because of the actions of their president Malawians will continue to suffer," the American singer said.
The remarks come after Banda attempted to declare the presidential election "null and void", prompting fierce legal wrangling over her right to do so.