The underground museum is slated to open next year.
Bloomberg is the foundation's chairman. The New York Times says he made the lowest possible interest rate of less than 0.3 percent so it would qualify as a loan rather than a gift under federal rules.
The museum is estimated to cost around $700 million.
The foundation has received more than $425 million from state and federal government and the Port Authority. It's also raised over $450 million in private donations.
A spokeswoman for Bloomberg didn't immediately respond to a request for comment or say why he's making a loan rather than a gift.