Gaza's health ministry said Dr Hussam Abu Safiya, director of Kamal Adwan Hospital, was arrested by Israeli forces.
The announcement on Saturday came a day after Israeli troops stormed the hospital, forcing many staff and patients outside to strip in winter weather, according to the ministry.
Israel's army did not respond to questions about Abu Safiya.
On Friday, it denied claims it had entered or set fire to the complex and said it was conducting operations against Hamas infrastructure and militants in the area and had ordered people out of the hospital.
It repeated claims that Hamas militants operate inside Kamal Adwan Hospital but provided no evidence.
Hospital officials have denied that.
Israel has levelled much of the northern Gaza areas of Jabaliya, Beit Hanoun and Beit Lahiya. (AP PHOTO)
Kamal Adwan Hospital has been hit multiple times during the past three months by Israeli troops waging an offensive against Hamas fighters in surrounding neighbourhoods.
The ministry said a strike on the hospital earlier this week killed five medical personnel.
Israel's nearly 15-month-old campaign of bombardment and offensives has devastated Gaza's health sector.
The war has killed more than 45,400 Palestinians, more than half women and children, and wounded more than 108,000 others, according to Gaza's health ministry.
Its count does not distinguish between civilians and combatants.
Abu Safiya was detained Friday along with dozens of other staff from the hospital and taken to an interrogation centre, the ministry said.
On Friday, MedGlobal, the humanitarian organisation where Abu Safiya worked, said he was a lead physician for the group and was gravely concerned about him.
The group said the incident follows the October detention of five other of its staff, calling it an "alarming and egregious pattern of targeting medical personnel and spaces."
Since October, Israel's offensive has virtually sealed off the northern Gaza areas of Jabaliya, Beit Hanoun and Beit Lahiya and levelled large parts of them.
Tens of thousands of Palestinians were forced out but thousands are believed to remain in the area in Beit Lahiya where Kamal Adwan and two other hospitals are located.
Israel has vowed to destroy Hamas after the militants' October 7, 2023, attack on southern Israel in which they killed about 1200 people and abducted some 250 others.
About 100 Israelis remain captive in Gaza, around a third believed to be dead.
On Saturday, Israel continued attacks across Gaza.
An overnight strike killed at least nine people in Maghazi, including women and children, according to an Associated Press reporter who saw the bodies and staff at Al Aqsa Martyrs Hospital where they were taken.
Israel said its troops had also begun operating in the northern city of Beit Hanoun, following intelligence that fighters and Hamas infrastructure were in the area.
Strikes also continued into Israel.
Early on Saturday morning, air raid sirens once again awoke Israelis and the military said it intercepted a missile fired by Yemen's Houthi rebels.
Israeli warplanes bombed key infrastructure in Yemen again on Thursday.
The Iran-backed Houthi rebels have also been attacking shipping in the Red Sea and say they will not stop until Israel agrees to a ceasefire in Gaza.
