Severe overcrowding apparently caused the crush as more than 12,000 people gathered at the temple to celebrate a Hindu festival, Jodhpur Police Superintendent Malini Agarwal said.
At least 168 people were killed in the stampede, said Naresh Pal Gangwar, the district collector.
The stampede apparently began as false rumors of a bomb spread among the crowd, said Ramesh Vyas, a pilgrim who was standing in line. India has been hit by a spate of recent bomb attacks, the latest on Monday night in the western city of Malegaon.
Television footage from Jodhpur showed dozens of bodies lying on the sidewalk, while nearby frantic people tried to revive unconscious devotees, slapping their faces and pressing on their chests.
Others dragged people by their arms and legs, running down a ramp that leads to the temple inside the massive 15th century Mehrangarh fort that overlooks the town.
One child sat on the ground next to the body of a woman, rubbing her forehead and crying "mother, mother."
"Several people fell down as the floor became slippery with thousands of devotees breaking coconuts for offering at the temple," said Ramesh Vyas, a witness.
The injured have been admitted to half a dozen hospitals in Jodhpur.
Thousands had gathered at the temple at dawn Tuesday to mark the first day of Navratra, a nine-day Hindu festival to honor the Mother Goddess.
Jodhpur is some 180 miles southwest of the Rajasthan state capital of Jaipur.
The Mehrangarh fort is one of the town's biggest tourist attractions with its huge walls, ornate interiors and views overlooking Jodhpur's "blue city."
Deadly stampedes are a relatively common occurrence at temples in India, where large crowds sometimes hundreds of thousands of people congregate in small areas lacking facilities to control big gatherings.
In August, 145 people were killed when rumors of an avalanche sparked a stampede at a hilltop temple in northern India.