The United Nations refugee agency, UNHCR, said it was "deeply concerned" by the clashes that erupted on Saturday when a demonstration against an Eritrean government event turned violent, injuring over 200 people.
The clashes began when hundreds of anti-government Eritreans came to prevent the event from taking place in Tel Aviv, the commercial centre of Israel.
"UNHCR calls for calm and restraint, and on all parties to refrain from taking any steps that could aggravate the situation further," William Spindler told reporters in Geneva.
While stressing that it was "important to establish accountability" for the events, he warned Israel against taking broad measures against Eritreans in the country.
"Any decision impacting all Eritrean asylum-seekers, or instances of refoulement would contravene international law," he said.
Collective punishment is banned under international law, as is refoulement, or returning someone to a country where they could face torture, cruel, inhumane or degrading treatment or punishment.
His comments came after Israeli Prime Minister Benjamin Netanyahu said the country was considering deporting 1,000 Eritreans who took part in the clashes.
Stressing that the situation in Eritrea, considered one of the world's most authoritarian states, "remains unchanged," Spindler warned that sending people back there "could result in dramatic human consequences."
He insisted that "the vast majority of asylum-seekers living in Israel are peaceful and law-abiding."
"The incidents on September 2 are deeply regrettable, and do not reflect the behavior of the broader Eritrean community in Israel."
According to June statistics, there are 17,850 Eritrean asylum seekers in Israel.
UNHCR said more than 170 asylum-seekers and dozens of police officers were injured in Saturday's clashes.
The U.N. rights office meanwhile decried the use of force by law enforcement.
"We understand that hospitals are reporting that there are people who suffered gunshot wounds, ... so live ammunition was used," rights office spokeswoman Ravina Shamdasani told reporters.
"We are alarmed at the high number of injuries and we insist that it is crucial that investigations take place, and that hate speech is avoided, including by the authorities," she said, also demanding that "the principle of non refundable is respected fully."