More than 100 people were injured in the chaos where tens of thousands thronged to the Galilee tomb of second-century sage Rabbi Shim Bar Yochai for annual Lag B'Omer commemorations that include all-night prayer, mystical songs and dance.

Witnesses said people were asphyxiated or trampled in a tightly packed passageway around three metres wide on Friday, some going unnoticed until the PA system sounded an appeal to disperse.

Crowds packed the Mount Meron slope in defiance of COVID-19 warnings.

Medics said there had been a stampede in the men's section of the gender-segregated festival. Casualties included children.

Some of the dead had yet to be identified and family members of those attending the festival who were still missing called in to radio stations asking for assistance in finding them.

Witnesses described the chaotic scene.

"There was some kind of mess, police, screaming, a big mess, and after half an hour it looked like a scene of a suicide bombing attack, numerous people coming out from there on stretchers," 19-year-old festival-goer Hayim Cohen said.

"We were going to go inside for the dancing and stuff and all of a sudden we saw paramedics from (ambulance service) MDA running by, like mid-CPR on kids," Shlomo Katz, 36, said. He then saw ambulances come out "one after the other".

Videos posted on social media showed chaotic scenes as ultra-Orthodox men clambered through gaps in sheets of torn corrugated iron to escape the crush. Bodies lay on stretchers in a corridor, covered in foil blankets.

An injured man lying on a hospital bed described to reporters how the crush began when a line of people in the front of the surging crowd simply collapsed.

"A pyramid of one on top of another was formed. People were piling up one on top of the other," he said.

"I was in the second row. The people in the first row - I saw people die in front of my eyes."

The Justice Ministry said investigators would look into whether there had been any police misconduct connected to the tragedy.

A police spokesman said overall capacity at Mount Meron was similar to previous years but that this time bonfire areas were partitioned-off as a COVID-19 precaution.

That may have created unexpected choke-points on foot traffic, Israeli media said.

Prime Minister Benjamin Netanyahu, while visiting the site, called it one of the "heaviest disasters" in Israel's history and promised a thorough investigation to ensure it did not recur.

He called for a national day of mourning on Sunday.

Australian Associated Press