The ship MSV Shiv Sagar MNV 2169 sank near the southern Dhofar region of Oman yesterday, local media reports said.
Six sailors were rescued after the Omani coast guards and naval vessels launched a rescue operation but nine others are still missing, the Gulf news reported.
The southern Dhofar region was hit by torrential rains this week, flooding the region and killing 12 people.
The Met authorities in the region had on Friday cautioned fishermen and other seafarers to check the condition of the sea over the next 24 hours before venturing out.
The rescued sailors were initially taken to the Sadah Hospital for treatment.
They were being kept at the police station in Sadah city, which is located around 140 km from Salalah in southern Oman as the rescuers searched for the missing.
The nine missing sailors were identified as Captain Prabhulal, Engineer Suresh, Lalji, Bharat, Mohan Mehta, Ashraf Asam, Yusuf Saamra, Suleiman Haji Sumara and Hussain Sumaraa.