The body was recovered from the drain near a factory in the industrial area under the Anantpura police station on Thursday morning.
The dead has been identified as Raju Bairwa, a resident of Hariom Nagar in the city.
Accusing him of theft, the accused had beaten the victim to death on Monday night.
The accused, identified as Devendra Meghwal, an auto driver; Radheshyam, a labourer; and Shambhu Singh, a guard at a factory, had thrashed him with sticks and rods, resulting in his deaths, police said.
Later, the body was dumped in a drain.
One of the three accused, Devendra Meghwal, on Wednesday night told about the incident to his friend Rahul Choudhary, who informed police.
Police have lodged a case of murder under Section 302 of the IPC.
Police teams are searching for the accused, said Inspector Pushpendra Jhanjhadiya.
The body has been handed over to family members after a post-mortem by a medical board on Friday morning, he added. PTI CORR RDK