John Philip, a fuel station employee who hailed from Kerala, was found dead by the Royal Oman Police (ROP) on Wednesday.
Philip had been missing since last Friday and police was searching for him since Saturday after a colleague reported him missing, the Times of Oman reported.
"His body was found. He was murdered," a senior police official said, adding investigation is on.
Money between OMR4,000 and OMR5,000 (over Rs 6,50,000) is missing from the station he used to work in, officials from the victim's company said.
Philip, who had been working in Oman for the last 13 years, is survived by his wife Binu and their two children.
His relatives had approached the Kerala government and the Indian government to trace him.