Trevor Neilson, philanthropic and political adviser for Jolie and her partner, Brad Pitt, told The Associated Press in New York on Monday that "hundreds of thousands of dollars" were missing.
He was responding to allegations by Mounh Sarath, director of Cambodian Vision in Development, that Jolie had reneged on an agreement by stopping funds for his group.
Neilson denied the 31-year-old actress had broken any agreement with Mounh Sarath.
"The sad reality is that this person who made these allegations was fired because we believe (he) stole" Jolie's donations, he said. He didn't elaborate or say whether action would be taken to recover the funds.
Mounh Sarath denied the allegations and said he "will fight any lawsuit to find out the truth and to see if they have any documented proof of the money stolen."
Jolie has promised up to $1.3 million over five years for a forest conservation program that was approved by the Cambodia government in 2003.
She terminated the contract with Cambodian Vision in Development in December, and has set up an independent Cambodian organization to administer the conservation project for remote northwestern areas of Cambodia, Stephan Bognar, executive director of the Maddox Jolie Project, said Monday.
The Maddox Jolie Project is named for Jolie's 5-year-old son, Maddox, who was adopted from Cambodia in 2002.
Scenes for her 2001 movie, "Lara Croft: Tomb Raider," were filmed at Cambodia's famed Angkor Wat temple.