The Millennium Challenge Corporation announced the power projects in January.
U.S. Embassy spokesman Benjamin Canavan said officials from the program - which dates from George W. Bush's United States presidency - and the Malawi government have been working for three years "to develop a much-needed investment for Malawian people in the power sector."
Caravan did not say what was holding up the agreement nor when it would be finalized.
The delay comes after the German government announced it was decreasing aid to Malawi following Malawi's failure to repeal laws that criminalize homosexuality, and its enactment of laws seen as restricting media freedom.
In Washington, Regan Lachapelle, spokeswoman for the Millennium Challenge Corporation, said it was concerned about "pending legal changes in Malawi and seeking clarification from the government about those changes." She did not elaborate.
"We remain in dialogue with the Malawi government," Canavan said, adding the Millennium Challenge Corporation is committed to "working with nations that are committed to good governance, economic freedom and investments in their citizens."
Malawi, among the world's poorest countries, was condemned around the world for 14-year-sentences handed out to a gay couple on charges of unnatural acts and gross indecency. President Bingu wa Mutharika later pardoned them, but said it was only on "humanitarian grounds" and expressed support for his country's anti-gay laws. At the time, U.S. presidential press secretary Robert Gibbs said the convicted men weren't criminals and called for an end to persecution and criminalization" of sexual orientation and gender identity.
Dozens of African countries have anti-gay laws.