Mohammad Aba Salmiya, director of the Al-Shifa Hospital, was detained on Thursday along with several doctors while they were evacuating to the south.
The Israel Defense Forces (IDF) said he was being questioned after evidence was uncovered “showing that the Shifa Hospital, under his direct management, served as a Hamas command and control center”.
“The Hamas terror tunnel network situated under the hospital also exploited electricity and resources taken from the hospital,” the IDF said in a statement.
“In the hospital, under his management, there was extensive Hamas terrorist activity. Findings of his involvement in terrorist activity will determine whether he will be subject to further questioning.”
The Telegraph has analysed and geolocated a tranche of footage released by the Israel Defense Forces (IDF) which does show tunnels with inter-connected rooms beneath the hospital.
While the footage does prove the existence of tunnels underneath the complex, it remains unclear whether they formed part of a Hamas command centre, as Israel claims.
After Mr Salmiya’s arrest, Gaza’s health ministry said it would stop coordinating with the World Health Organisation (WHO) on any future evacuations of medical staff and patients from Israeli-besieged hospitals.
“We are deeply surprised by the position of the UN and the WHO which have not provided any explanation for this crime.”
Before gaining control of Al-Shifa last week, Israel alleged that the Israeli-built hospital served as the headquarters for Hamas.
Israeli forces in recent days laid siege to the hospital and later raided it. Snipers posted on nearby roofs were allegedly shooting at anyone trying to move from one wing of the hospital to another.
IDF representatives this week showed reporters underground rooms where they claimed the fighters were holed-up and kept some of the prisoners.
But the evidence published so far does not yet corroborate Israel’s assertion that Al-Shifa served as Hamas’s nerve centre.
In one video published on the IDF’s official social media channels, IDF spokeswoman Masha Michelson, wearing olive green body armour and a helmet, shows off an array of captured Hamas weaponry, drones and laptops.
She enters an unlit tunnel, consisting of “multiple rooms”, including a bathroom and a kitchen area.
Despite Ms Michelson insisting her footage is evidence that “Hamas uses this place as a command and control centre”, there are no visible signs of any human activity in any of the rooms on the visual tour.
The walls of the cramped, concrete tunnels are bare and there is no rubbish on the floors of the underground facility, a sign that it hasn’t been used recently.
One of the rooms is tiled with a sink fitted to a steel cabinet, similar to those found in medical facilities.
An aerial shot, featured in a second IDF video, shows the entrance to the tunnel system nestled in a crater alongside the Al-Shifa.
Israeli soldiers take viewers deeper into the underground labyrinth, again only showing entirely empty shells of passages void of any signs of life.
A third video offers more proof that the network of tunnels had been used more recently, as an IDF cameraman clambers over piles of belongings strewn across the floor of a civilian house.
In one room, a group of heavily-armed Israeli troops stand over a set of stairs heading down into a dark tunnel, an empty plastic bottle of drink occupying the first step.
The footage, however, stops short at a metal, spiral stairway heading into the darkness below.
Instead, bringing the viewer back into the building above, which resembles a school with used chalkboards and English-language posters on the wall.
Standing in another stretch of the tunnel network, which was said to be 300 metres long, an IDF spokesman claimed “all the gear was evacuated” from empty rooms, which appeared to be a series of toilets and showers.
The video ends at a spiral, metal staircase similar to the one shown entering the tunnels from a civilian house.
Israel has been under increasing international pressure to back-up its claims that Hamas had built a terror base under the besieged hospital.
The facility endured a large-scale assault by the IDF, forcing the evacuation of vulnerable patients amid heavy bombardment of the surrounding area.
CCTV footage showing hostages being taken into Al-Shifa had been released by Israel to justify its claims.
The hospital was originally built when the State of Israel had full control of the area.
Israel’s former Prime Minister Ehud Barak told CNN earlier this week that some of the underground space underneath Al-Shifa was built by Israeli engineers.
Israeli officials said that Hamas dug several further floors and added more tunnels to the basement areas originally built in the 1980s.