The Israeli military confirmed that it had struck the Jousieh crossing in Lebanon's Bekaa area, where a road leads to Syria, saying it was being used by Hezbollah to transfer weapons.
The overnight airstrike hit Hezbollah "infrastructure" at the land crossing between Syria and Lebanon, the Israeli military said in a statement.
But the Lebanese authorities warned that the Jousieh crossing was no longer functional, the UN refugee agency said.
"This is hindering and really putting at risk a main lifeline that people use to escape the conflict in Lebanon and cross into Syria," said Rula Amin, Middle East spokeswoman for UNHCR.
This "is the only route these people have to escape Lebanon", Amin told a media briefing in Geneva via video-link from the Jordanian capital Amman.
Amin said the Jousieh strike hit within 500 metres (550 yards) of the immigration office, with no prior notification given.
It is the second such gateway hit by the Israeli army this month.
It had previously struck the Masnaa crossing further south, leaving it unusable.
"It means people have to think twice before they attempt to cross, on how safe their route is," said Amin.
- 'Catastrophic' -
Israel has been at war with Hezbollah in Lebanon since late last month, in a bid to secure its northern border after nearly a year of cross-border fire from the Iran-backed armed group.
Nearly 500,000 people have fled to Syria after Israel launched an intense air campaign mainly on Hezbollah bastions in Lebanon in late September, Lebanese official figures show.
Amin said that around 70 percent of those fleeing across the border were Syrians, with the rest largely Lebanese.
"The suffering of those people crossing does not end at the border. Unfortunately there's another emergency and humanitarian catastrophe unfolding at the final destinations where these people are crossing to," she said.
More than 90 percent of the Syrian population needs humanitarian assistance, Amin added, describing the situation as "catastrophic".
Many people displaced by the conflict have no home to return to, as Israeli bombings have devastated border villages, towns and cities like Tyre, she said.
"People's ability even to go back their homes once this conflict is over has been hindered," Amin said.
"The loss of options on how to stay safe is just so profound, it's sad. It's not right, it's unacceptable."
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