The reports were amended late Monday after receiving inquiries from The Washington Post.
The newspaper said Clinton has failed to report the charity five times since it was established in 2001.
A Clinton's spokesman said the senator's failure to report the existence of the family foundation was an oversight, the Post said.
Clinton serves as treasurer and secretary of the family foundation, which was seeded with $5.16 million of the family's own money. The foundation has given away $1.25 million in charitable contributions, the newspaper said.
The Post said the family foundation is separate from the William J. Clinton Foundation, which has directed $10 billion in corporate money and resources to groups working on the issues of AIDS, climate change, hunger and poverty.