The BBC's Damian Grammaticas in Delhi says this is the fourth time this year that lives had been lost - probably needlessly - during a stampede at a religious festival in India.
He says crowd control at such events is usually rudimentary and the police simply not trained in effective crowd management.
Last month 140 pilgrims were killed in a stampede at a mountain temple in the northern state of Himachal Pradesh.
The Chamunda Devi temple is inside the huge 15th Century Mehrangarh Fort, high above Jodhpur's "blue city".
It is popular with tourists and local people - particularly at this time, the start of the nine-day festival of Navaratra.
Before dawn, thousands of people had made their way to the hill-top temple overlooking the city.
It is not entirely clear why the stampede happened, but something triggered panic among men queuing in the narrow lane leading to the temple.
Hundreds rushed down the hill crushing those waiting at the bottom.
"I was at the temple in a queue of people when, suddenly, people bunched up into one another and there was shoving and pushing," one survivor, Daulat Singh, told the BBC Hindi service.
"We fell on the ground, and on top of us, some 30 or 40 men fell. It was difficult to get people out."
Another man, Naresh Kumar Meena, said: "In front of the temple, there was some bamboo railing which collapsed. As soon as that happened, everyone near to it fell. There were also people pushing from behind."
Police and volunteers spent hours ferrying the injured for treatment
One official in Jodhpur said the collapse of a wall on the narrow path leading to the temple caused people to flee. There were also false rumours of a bomb, reports said.
Rajasthan's Home Secretary SN Thanvi said: "The stampede began when people lost their footing and set off a chain reaction."
Television footage showed dozens of injured littering the streets.
With no first aid available at the scene, people tried desperately to resuscitate the unconscious as others scooped up bodies and took them to hospital.
"When I arrived, I saw chaos, people running around the place. I was looking for my friend and after a while found him," local student Manish said.
"He was unconscious but without serious injuries."
The authorities have ordered an investigation into the incident.
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