JERUSALEM, Apr. 1 (Reuters) - Israeli forces left Al Shifa Hospital in Gaza City on Monday after a two-week operation by special forces who detained hundreds of suspected Palestinian militants and left a wasteland of destroyed buildings.

With access to Gaza's biggest hospital severely restricted, the Israeli and Palestinian versions differed sharply.

Palestinian officials called the raid on a hospital treating severely wounded patients a war crime, while Israeli officials said special forces units conducted a targeted strike against a Hamas stronghold deliberately located among vulnerable civilians.

Thousands of Palestinians - 6,200 according to the Israeli military - had been sheltering in the complex, one of few locations in the north of Gaza with some access to electricity and water.

Ismail Al-Thawabta, director of the Hamas-run Gaza media office, said Israeli forces had killed 400 Palestinians in and around the hospital including a woman doctor and her son, also a doctor, and put the facility out of action.

"They bulldozed the courtyards, burying dozens of bodies of martyrs in the rubble, turning the place into a mass graveyard," he said. "This is a crime against humanity."

Hamas and medics deny any armed presence in hospitals but Israeli military spokesperson Daniel Hagari said the site had been turned into a major operating centre by the Palestinian armed groups Hamas and Islamic Jihad.

He said emergency patients had been evacuated from the hospital before the operation and said no Palestinian civilians, patients or medical personnel had been harmed by Israeli forces.

He said three of the main buildings in the complex had been destroyed in the fighting - the main emergency room, the maternity ward and an annexe known as the Qatari Building - after Hamas fighters refused calls to surrender.

"They're using those places, they know it's a safe haven, they know that they use it intentionally as their command and control centre," he told reporters on Monday.

He said 200 militants and two Israeli servicemen had been killed during the operation and more than 900 suspected militants detained, of whom some 500 were identified as Hamas or Islamic Jihad, including senior commanders and officials.

He said documents recovered by Israeli forces showed the hospital was used as a base to control the northern section of the Gaza Strip, which has largely been destroyed since the start of the ground invasion in October.

As well as weapons and computers equipment, cash worth more than $3 million was also recovered, he said.

"It was a significant operation in terms of the blow that Hamas and Islamic Jihad suffered," Hagari said.

Photo from Reuters