The director of Al Shifa Hospital in the Gaza Strip was being questioned on Thursday over evidence the Israeli military said showed the facility had been used as a command and control centre for the Islamist movement Hamas.
The military said Dr Muhammad Abu Salamiyah had been in charge of the sprawling complex as Hamas militants built up a network of military infrastructure and stored weapons inside the hospital and its grounds.
"In the hospital, under his management, there was extensive Hamas terrorist activity," it said in a statement.
Shifa Hospital, the biggest medical facility in the Palestinian Territories, has been at the centre of accusations of war crimes on both sides.
While Israel says Hamas has located its operational structures at the site, in contravention of international law, Palestinians have accused Israel of targeting a medical facility where thousands of civilians had sought shelter from air strikes that have killed thousands.
Israeli troops entered the complex earlier this month and uncovered what they said was at least one well-equipped tunnel as well as a quantity of weapons which it said showed how the hospital was used by Hamas.
Hamas and doctors at the hospital have previously denied accusations that the complex was used for military purposes and dismissed the evidence presented by Israeli officials.
The Palestinian health ministry said Abu Salamiyah and a number of doctors were arrested at dawn at a checkpoint on the road linking northern Gaza to the south, where Israel has told Palestinians from the north to move for their own safety as its military operation continues.
The army was still questioning him, army spokesman Lieutenant Colonel Richard Hecht told reporters on Thursday afternoon. He said Abu Salamiyah was not under indictment and no one was suggesting he was a member of Hamas.
"We took him to ask him a few questions about why under his hospital there was so much terrorist activity above ground and underground," Hecht said.
Palestinian Health Minister Mai Al-Kayla said the arrests showed that Israel was flouting international humanitarian law. She said Palestinian authorities had appealed to the United Nations as well as bodies including the Red Cross, asking them to put pressure on Israel to reverse course.
Hamas also issued a statement condemning the arrests of the doctors, who it said had remained in the hospital to facilitate the evacuation of patients and wounded.
"We call on the Red Cross and international organizations to work for their immediate release," it said.
