World Vision questioned Tuesday Israeli accusations that tens of millions of dollars in aid were funnelled off to the Islamist movement Hamas, calling the alleged sum "hard to reconcile" with reality.
An Israeli court on Thursday charged the NGO's Gaza head Mohammed al-Halabi with funding "terror".
According to the Shin Bet internal security agency, he diverted $7.2 million (6.5 million euros) each year since 2010 to Hamas and its military wing, though the charge sheet does not specify an amount.
Part of it was allegedly used to build attack tunnels from blockaded Gaza into Israel.
World Vision International president Kevin Jenkins said in a statement the organisation was conducting an investigation into the allegations and "condemns any diversion of funds from any humanitarian organisation".
"If any of these allegations are proven to be true, we will take swift and decisive action."
But he said the organisation "have not seen any of the evidence," and suggested the numbers were exaggerated.
"World Vision's cumulative operating budget in Gaza for the past ten years was approximately $22.5 million, which makes the alleged amount of up to $50 million being diverted hard to reconcile," the statement read.
The NGO has suspended its operations in Gaza.
The statement said Halabi became the NGO's Gaza head in 2014 and would have only had the personal authority to sign off a budget up to $15,000.
The NGO said it carried out extensive background checks on its staff.
Halabi's lawyer has also rejected the accusations as baseless, saying his client was held without charge or access to legal support for several weeks after his June 15 arrest.
The NGO has 150 staff across Jerusalem, the West Bank and Gaza, providing aid to around 560,000 people. The group said its work helped more than 92,000 children last year.