Syria’s UN ambassador on Thursday accused Israel of assisting Salafist and other Islamist groups in Syria to overthrow the government in Damascus.

At a special public Security Council hearing called to address the humanitarian challenges in the war-torn country, Bashar al-Ja’afari said that Israel had given medical aid to Salafist and Islamist rebels and returned them to the battlefield.

“Israel [has a] partnership with Salafi, Takfiri and terrorist groups, allowing those armed groups to cross the separation line in the occupied Syrian Golan and treating their wounded in Israeli hospitals and returning them to the Syria territory through the separation line anew,” Ja’afari said.

He also accused Western intelligence agencies of aiding Syrian rebels who had “spread destruction and sabotage and shed innocent blood there too.”

Ja’afari’s comments echoed Syrian President Bashar Assad, who told a Syrian television station Wednesday that the West was backing al-Qaeda against his embattled regime.

Ja’afari’s comments were apparently referring to two separate instances in recent weeks in which wounded Syrians were allowed across the border into Israel for medical treatment.

The Syrians were later returned across the border, amid reports that the IDF was setting up a field hospital along the frontier for future cases.

Israel officials refused to say whether the Syrians who entered Israel were fighting on the side of the rebels or that of Damascus.

While hundreds of thousands of refugees have fled Syria into Lebanon, Turkey, Jordan and Iraq, Israel has kept its borders closed, with officials saying the cases of the wounded being let in for treatment did not change that policy and were isolated humanitarian cases.

Israel reportedly struck a convoy of weapons reportedly en route to Hezbollah and has struck back at Syrian positions after mortars landed in Israeli territory, but has mostly stayed out of the conflict.

Netanyahu told the BBC Thursday that it is Israel’s right to keep weapons from falling into the wrong hands in Syria. Officials have also raised concerns over hardline Islamist groups taking over areas near Israel’s northern border.

“The main arms of concern to us are the arms that are already in Syria — these are anti-aircraft weapons, these are chemical weapons and other very, very dangerous weapons that could be game changers,” Netanyahu said.

The prime minister added that “we are not aggressive. We don’t seek military confrontation, but we are prepared to defend ourselves if the need arises… and I think people know that what I say is both measured and serious.”

At the UN meeting, the body’s chief humanitarian official asked the Security Council to approve cross-border relief operations into Syria to deliver aid to millions of suffering civilians.

It was the focus of a public briefing by the UN agency chiefs for humanitarian affairs, refugees, women in conflict, and children in conflict, who used the Security Council platform as a way of speaking over the heads of the deadlocked council nations to appeal to the world for pressure to allow relief for Syria’s civilians.

The agency chiefs launched their campaign Monday with an op-ed in The New York Times that said: “There still seems to be an insufficient sense of urgency among the governments and parties that could put a stop to the cruelty and carnage in Syria.”

The Security Council has been deadlocked for months on the Syrian war, and did not act or make any statement after Thursday’s briefing.

Western and Arab nations blame the conflict on Assad’s government. Russia insists on assigning equal blame for the suffering to the Syrian rebel opposition, and has cast vetoes, along with China, to block draft council resolutions.

Undersecretary-General for Humanitarian Affairs Valerie Amos said, “We were told, just in the last 24 hours, that the (Syrian) government now requires two ministers to sign off the movement of every single truck. This is going to make our job completely impossible.” She said children are starving to death in Syria for want of food aid.

The UN High Commissioner for Refugees, António Guterres, warned the council that without an end to the fighting soon, almost half of Syria’s 20.8 million population could be in need of humanitarian help by the end of 2013.

Guterres said 400,000 refugees had fled Syria in the last seven weeks, bringing the population of Syrians registered as refugees or waiting to be registered to 1,367,413. If current trends continue, he said, then by the end of the year there may be up to 3.5 million Syrian refugees, together with 6.5 million people inside Syria who could become in need of help.

“These figures are terrifying,” Guterres said.

In the past few weeks, the humanitarian agencies have separately warned that their resources are running low, and that without additional funds they will be forced to scale back relief efforts.

About half of the $1.5 billion needed to fund Syria’s humanitarian needs through June has been collected, Amos said, largely thanks to a recent $300 million pledge from Kuwait.

Amos said 6.8 million Syrians are in need, with 4.25 million displaced within Syria and 1.3 million as refugees in neighboring countries.

The UN special representative of the Secretary-General on Sexual Violence in Conflict, Zainab Bangura, said women in Syria have been “raped, tortured and humiliated.”

“Many have attempted to commit suicide,” she added.

On Wednesday she presented a report to the council that accused Syria’s military and intelligence forces and an allied militia of using systematic sexual violence on women.

She said Thursday that Syria had brought one instance of the rape of a Syrian woman by opposition forces to her attention.

Bangura urged the opposition Free Syrian Army to issue orders to its fighters to respect women and hold rapists accountable, and made the same demand of Syrian government forces and its Shabbiha militia.