Thirty-one people were injured after flight EY474 from Abu Dhabi ran into unexpected turbulence about 45 minutes before landing at Soekarno-Hatta International Airport on Wednesday, Etihad said.
Most of the passengers were Indonesian Muslims returning from a minor pilgrimage known as umrah in Saudi Arabia.
"Three pilgrims suffered spinal fractures," Edi Suryono, a doctor at the airport's clinic, was quoted as saying by BeritaSatu.com news website.
Several other passengers had difficulty breathing and bruises to the head, he said.
Photos taken by a passenger, posted on Twitter, showed broken overhead bins and oxygen masks dropping.
The turbulence occurred soon after passengers finished a meal and many were not wearing seatbelts, the report said.
Passengers recounted terrifying scenes on the plane.
"Suddenly my body was jolted up and down and my head hit the ceiling until it cracked," Lita Herlita, a 42-year-old pilgrim was quoted as saying by Kompas daily.
"I feel sorry for old women who were hit by big bags. There was blood on their heads and some had broken bones."
"We could only scream "Allah, Allah ya Allah. I thank God I'm still alive."
"It was the scariest turbulence experience I've ever had," a passenger named Ari, whose father was badly injured, wrote on Twitter.
"Everyone started to cry, terrified along with the screams, some people shouted "Allahu Akbar! (God is Great)" as they were ready to die," he tweeted in English.
Mardjono Siswosuwarno, an investigator with the Indonesian Transport Safety Committee, said the incident was being investigated but that the turbulence was likely caused by a meeting of two bodies of air moving at different speeds, rather than a visible storm.
"It looked like clear-air turbulence so it was unexpected," he said.