Commenting on the issue in general, Sari Bashi, Israel and Palestine country director at Human Rights Watch, told Al Jazeera how provisions that “suspend due process protections for suspects”, intended for “emergency situations”, are used “quite routinely against Palestinian detainees”.

The Shin Bet charges against Halabi have been denied by his family members. His father Khalil has told reporters that the charges were based on “misinformation provided by a disgruntled World Vision employee”.

Christian-charity 'top-of-Israel's-target-list'

Hamas also has denied any links to Halabi, and called the allegations “lies”.

Last week, World Vision said that “based on the information available to us at this time, we have no reason to believe that the allegations are true”. On Monday, World Vision International CEO Kevin Jenkins pointed to discrepancies in the Shin Bet charges: “World Vision’s cumulative operating budget in Gaza for the past 10 years was approximately $22.5m, which makes the alleged amount of up to $50m being diverted hard to reconcile.”

In addition, “Mohammad el-Halabi was the manager of our Gaza operations only since October 2014. Before that time he managed only portions of the Gaza budget.”

When pressed on whether “the Israeli government still stood by figures alleging approximately $50m had been taken”, an Israeli government spokesperson said the amount was irrelevant.

Speaking last week to Israeli newspaper Haaretz, Halabi’s lawyer suggested that armed Hamas members had stolen from the organisation’s depots, but that the charges against his client were significantly “inflated”.

World Vision has long been an enemy for pro-Israel groups who, in the words of one lobbyist, believe the group “assists Hamas in its propaganda war against the Jewish state”. A US-based, pro-Israel think-tank has listed World Vision as part of an NGO “jihad” against Israel.

NGO Monitor, a group that plays a key role in the escalating intimidation of local and international human rights groups and NGOs in Palestine/Israel, accused World Vision back in 2004 of “encouraging or at least condoning terrorism and incitement”.

It is that wider context of a crackdown on humanitarian groups and human rights defenders that worries Palestinians and other observers.

Israeli minister Gilad Erdan has claimed that the accusations against Halabi prove the government’s claim that “there are extensive ideological and monetary ties between terrorist organisations and delegitimisation organisations that work against Israel”.

World Vision, like many other international organisations, has been clear in its call for Israel to end its blockade of the Gaza Strip, and has also spoken up on other issues, such as the forcible transfer of Palestinians in the occupied West Bank.

At al-Mezan in Gaza, Zaqout is clear about why Israel has targeted World Vision in this way: “The Israeli government and [Shin Bet] are using very dirty tools in order to harass and pressure both Palestinian civil society and international NGOs.”

Senior UN official Robert Piper has stressed the need for a “prompt, thorough, independent, impartial and transparent” legal process. Some, however, wonder how the court will reach “anything but a foregone conclusion”, given the experience of Palestinians in both military and civilian courts.

Last week, Israeli authorities claimed that as part of the World Vision investigation, information was obtained implicating “other humanitarian aid organisations”. Israeli officials have also accused an employee of Save the Children of being recruited by Halabi for Hamas.

Israeli authorities are also reportedly “preparing to release information soon on a United Nations organisation Israel also alleges is linked to Hamas”.

A senior British NGO official, familiar with the situation in Gaza, told Al Jazeera: “This is about Israel trying to put international NGOs, who are increasingly critical of Israeli policies, in their place. It is possible that World Vision, with its strongly evangelical supporter base in the US, was simply top of Israel’s target list. The question is: Which NGO is next?”