Amnesty International has warned Israel not to continue with a "secret trial" of the Christian charity World Vision's Gaza director amid reports that media and the charity's staff were barred from the trial and an undisclosed allegation of mistreatment in custody.

Yesterday, Mohammed al-Halabi, the NGO's Gaza director, was brought before a pre-trial hearing in Bir al-Saba, a city in the south of present-day Israel as his lawyer told told the AFP news agency that all media and World Vision staff were barred from attending.

Amnesty claimed that al-Halabi, who is facing 12 charges including being a member of a terrorist organisation – Hamas' armed wing, Izzedin al-Qassam – and siphoning off the charity's funds for terrorism purposes, was initially denied access to a lawyer. Then, when he was allowed to meet a legal representative, al-Halabi allegedly said that he had been "seriously mistreated in custody," according to Amnesty.

Amnesty went on: "The lawyer is prevented from disclosing the details of that allegation, as well as many other elements of the case, by a set of severe restrictions imposed by the Israeli authorities on reporting around the case."

Magdalena Mughrabi, deputy director of the Middle East and North Africa programme at Amnesty International, said: "Secret trials are the most flagrant violation of the right to a public hearing. Holding these court proceedings behind closed doors would render any convictions obtained unsound. The allegation of stealing money intended to help alleviate the humanitarian crisis in Gaza is extremely serious. This makes it all the more pressing to ensure that Mohammed al-Halabi's rights are fully respected and that his trial be fair and transparent."

Israeli authorities arrested al-Halabi on 15 June at the Erez crossing between Israel and Gaza, while while crossing the border into the enclave, which is under the de facto rule of Hamas, which is on the Israeli and US terrorism blacklists.

He was transferred to a detention centre at Ashkelon on Israel's south coast, where he was interrogated before being moved to Nafcha prison in the Negev desert.

Amnesty said that he was not permitted to see a lawyer until 6 July and therefore potentially faced three weeks of intensive interrogations without legal representation. He was charged on 4 August, more than seven weeks after his arrest.

Amnesty also pointed to reports that he was severely beaten and that his "confession" to stealing $7.4 million per year was obtained "under duress". Amnesty continued: "This appears to be a dubiously high figure, given that according to World Vision, Mohammed al-Halabi and other managers in his position only have the authority to authorize spending up to a maximum of $15,000 of the budget at a time and the organization's total Gaza budget for the last decade was approximately $22.5 million."

Mughrabi added: "The Israeli authorities must immediately investigate the allegations that Mohammed al-Halabi was mistreated in custody and may have been forced into 'confessing' under duress. Any evidence obtained through torture, or other cruel, inhuman or degrading treatment must be excluded from proceedings. Without independent and impartial investigations into these allegations the trial risks being fundamentally flawed".

According to the Israeli daily newspaper Haaretz, Western diplomats reportedly noted that Israel had "invested considerable efforts in briefings for the Israeli and international media [about aid agencies in Gaza]. However, it has invested hardly any effort in transferring information and evidence to its allies and closest friends in the world."

Earlier this month, Australia joined Germany in suspending funding for World Vision amid the allegations.

A UK Government spokesperson at the time stressed to Christian Today that the Department for International Development has not provided any funds to World Vision since the Israel-Gaza war of 2014.

Gaza's Palestinian Christian population is ancient but tiny, at around 1,200 people out of a total of 1.8 million.