The 43 peacekeepers from Fiji were forced to surrender their weapons and taken hostage near the Quneitra crossing, but 81 Filipino blue helmets "held their ground" and refused to disarm, the Filipino defense department said.
"This resulted in a stand-off which is still the prevailing situation at this time as UN officials try to peacefully resolve the situation," said a statement in Manila.
Syrian rebels, including fighters from the Al-Qaeda affiliate Al-Nusra Front, stormed the crossing at Quneitra sparking an exchange of gunfire with Israeli troops yesterday.
The UN Security Council "strongly condemned" the detention of the 43 and the "surrounding of positions" manned by the 81 other peacekeepers, by "terrorist groups and by members of non-state armed groups."
The council demanded the "unconditional and immediate release of all the detained United Nations peacekeepers" and urged countries with influence to help win their release.
The 81 Filipino troops were locked in a standoff near Ar Ruwayhinah and Burayqah, while the Fijian soldiers were taken to the southern part of the buffer zone, officials said.
"Some groups are self-identified as affiliated to Al-Nusra but we are not able to confirm," he said.
UN officials noted that the peacekeepers monitoring the armistice line between Israel and Syria were detained twice last year and released safely.
In June 2013, there was a similar takeover of the crossing by rebel forces, but the Syrian army managed to regain control.
Six countries contribute troops to the 1,200-strong United Nations Disengagement Observer Force (UNDOF): Fiji, India, Ireland, Nepal, the Netherlands and the Philippines.
The Philippines, which has 331 troops serving in UNDOF, announced on Saturday that it will pull out of the peace force, citing security concerns.
Last year, Manila also considered pulling its Golan peacekeepers out after 25 of them were kidnapped but later freed by Syrian rebels in two separate incidents.
A Filipino soldier was also wounded by a wayward shell last year.
Since the Syrian conflict erupted in 2011, the plateau has been tense, with a growing number of rockets and mortar rounds hitting the Israeli side, mostly stray, prompting occasional armed responses.
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