World Vision said in a statement on Thursday that “we have no reason to believe the allegations are true” based on the available information, and stressed that there was no suggestion the organization had been complicit in any diversion of funds.

Tim Costello, the chief executive of World Vision Australia, which has been deeply involved in the Gaza project, said his organization was nevertheless “very worried” about the impact the accusations would have on its ability to raise funds and work.

“We are profoundly shocked by these allegations,” Mr. Costello said. “We want to get to the bottom of this, we want the truth.”

Mr. Costello said he did not think it was appropriate for the Israeli authorities to publicly accuse Mr. Halabi and World Vision of the diversion before they had a chance to review the evidence. He added that Mr. Halabi was prevented from consulting a lawyer for the first 25 days of his detention.

“We just really want a fair process, where Mohammad, once charged, gets to present his side, because we want to know the truth about this,” he said. “The truth comes out when you hear both sides.”

Maj. Gen. Yoav Poly Mordechai, an Israeli official responsible for liaising on civil affairs in the West Bank and Gaza, met in Jerusalem on Thursday with World Vision leaders and presented them with the results of Israel’s investigation and a confession from Mr. Halabi, according to a statement released by General Mordechai’s office.

Hamas representatives were quick to dismiss the Israeli accusations, saying they had no faith in confessions obtained by Israeli intelligence officials, while maintaining that Palestinians were legitimately allowed to use all means to defend themselves.