World Vision believes more than 90% of its aid to Liberia went missing in a massive fraud.
Vice-President Geoff Ward has told the BBC the losses came to more than $US1 million. He pledged to make "every effort" to avoid a repeat.
A former senior World Vision official in Liberia and two others have been charged.
They are accused of selling the food in local markets and keeping the profits. They are also accused of using construction materials to build themselves multiple homes using labour provided by US-funded aid workers.
The thefts reportedly began in 2005, as Liberia emerged from 14 years of civil war that claimed some 300,000 lives. More than three million people were displaced.
World Vision is said to have received an anonymous tip-off about the fraud in early 2007. Auditors were sent to 258 Liberian towns believed to be benefitting from the programme.
Mr Ward told the BBC that they could only establish that 9% of the food aid had reached the intended recipients. The Associated Press reports that 34 of the towns did not even exist.
Mr Ward says documentation showing receipt of food aid had been "falsified in the offices of World Vision in Liberia in a very large way."
He said the organisation had now tightened its procedures - including launching a hotline for people to report any wrongdoing - to make such frauds more easily detectable in future.