"Clearly these boys need to be found, that's totally understandable, but the scale of operations and the number of people they are affecting is deeply disturbing," said its spokesman Rupert Coville.
"We reiterate our call for strict adherence to international law by all relevant actors and join others in their call for restraint," he told reporters.
The three teenagers went missing on June 12 near an Israeli settlement bloc close to the city of Hebron.
The Israeli army has launched a vast hunt for them, dubbed Operation Brother's Keeper
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Several Palestinians have been killed and dozens wounded so far.
The mothers of the three teenagers travelled to Geneva this week and held a private meeting with deputy UN human rights chief Flavia Pansieri.
"As a mother herself, she expressed her understanding of their deep anxiety about the fate of their sons. We are concerned that the three teenagers have still not been located, after being missing for 15 days. We hope for their immediate safe return," said Colville.
Colville said the loss of life during the operation was alarming, as were the spiking tensions in the West Bank.
"We call for prompt and thorough investigations, and prosecution of the perpetrators in cases where there has been excessive use of force," he said.
More than 380 Palestinians, two-thirds of them Hamas members, have reportedly been arrested by the army during the search, though Coville put the number at around 500.