The Vatican's representative in Jerusalem has accused Israel of "brutally violating" a decades-old agreement to uphold religious freedom.
It follows Friday's attack by Israeli police on the funeral of Palestinian-American journalist Shireen Abu Aqla.
Officers kicked and beat pallbearers and fired stun grenades into the crowd of mourners at St Joseph Hospital.
Monsignor Tomasz Grysa, who represents the Holy See in Jerusalem, said the action was unjustified and unprovoked.
Israel's police force said its handling of the funeral was being reviewed and accused religious leaders of making "extreme" statements.
Abu Aqla, a veteran Al Jazeera correspondent who was a Christian, was shot dead during an Israeli army arrest raid in the occupied West Bank on Wednesday.
At a news conference at St Joseph Hospital on Monday, the leaders of 15 denominations in Jerusalem condemned what they called the "violent intrusion" of Israeli police into Abu Aqla's funeral procession.
Monsignor Grysa said that a 1993 agreement between the Roman Catholic Church and Israel "upholds and observes the human right of freedom of religion, which in this case has been brutally violated".
Archbishop Pierbattista Pizzaballa, the top Roman Catholic cleric in the Holy Land, said: "The Israel Police's invasion and disproportionate use of force - attacking mourners, striking them with batons, using smoke grenades, shooting rubber bullets, frightening the hospital patients - is a severe violation of international norms and regulations, including the fundamental human right of freedom of religion."
St Joseph Hospital's director, Jamil Koussa, said it was now clear the target of police violence was the coffin itself, showing video of the beatings and new CCTV images of the hospital building being stormed by police, which he described as an attempt to "horrify people in the building".
The East Jerusalem hospital is famous for its maternity ward and known for its care for Muslim, Jewish and Christian families alike. The staff call it a "place of healing". But on Friday they were treating wounds among their own medical staff.
Many doctors and nurses had come outside to pay their respects to Abu Aqla when the Israeli forces surged into the compound.
Dr Mohammed Hmeidat, a doctor in the neo-natal intensive care unit, showed the BBC burns he suffered from a stun grenade.
"One of them was very close to my feet, and exploded. After that we hurried to the emergency department and also [the police] followed us to the emergency department," he said.
Israel's police force said: "Extreme statements, which include assertions about events that are still being examined, only stir up emotions and are not responsible.
"Police were present at the incident to maintain public order and to allow the funeral to take place, when there were extremists on the ground who provoked and engaged in an attempt to turn the funeral into a violent event," it added.
"We expect clerics to help calm the area and avoid statements that agitate it."
The force has defended its actions on the day. It has said 300 "rioters arrived" at the hospital, but this has claim been discredited. It has said some people threw stones and it was protecting the funeral plans agreed by the family to use a hearse.
It has said this is why it stopped the coffin being taken on foot from the compound. However, the family has categorically rejected the police version of events.
At Palestinian funerals, the coffin or stretcher is frequently carried by hand in public as a mark of popular tribute, especially at the passing of a notable figure. At such events it is also not uncommon for plans to change suddenly if more people want to pay their respects.
On Friday, the police claimed mourners threatened the driver of the hearse and then proceeded to carry the coffin against the wishes of the Abu Aqla family. It said: "Israeli Police intervened to disperse the mob and prevent them from taking the coffin."
But speaking to the BBC, Abu Aqla's brother Tony dismissed the police use of the family's wishes to justify its actions, accusing them of a "inhumane attack".
"Everybody saw the pallbearers beaten savagely by batons without any mercy, without any respect to the funeral, to the dead," he said.
"I never gave any promises to the Israeli police, this was a national funeral for all the Palestinians to participate in... They had no business to do at the gate [what they did]."
Another relative, Abu Aqla's niece Lina, revealed she had to run and hide in the hospital while trying to mourn.
"I honestly was very afraid... because they started throwing stun grenades, and one of them actually threatened to beat me if I don't move out of the way," she said.
Journalists who were with Abu Aqla and witnessed her death have said the gunfire came from Israeli troops.
Israel has said it is investigating, but it has maintained the fatal shot could have come its forces or Palestinian militants.