Police said the skeletal remains have been sent for a DNA test. (Representational)

The skeletal remains of a missing person was found in a septic tank in Maharashtra's Palghar district, police said on Saturday, adding one man from Kerala was arrested in the matter.

Sixteen-year-old Aminul Haque Mohammad Mumtaz Ali, a migrant farm labourer, had gone missing from Wada in Palghar on September 28, 2016 after which a case was registered, said Palghar police's assistant inspector Mansingh Patil.

"Our probe into Ali's call records showed that he had spoken to people in Kerala and Karnataka. We zeroed in on a few calls and on Friday managed to catch Ali's cousin brother Mansur Mohammad Akbar Ali (22) who is working in a brick kiln in Kerala," Mr Patil said.

"He has confessed to his role in Ali's disappearance and murder. He led us to the skeletal remains of Ali, in a septic tank, on Friday," the official said.

The skeletal remains have been sent for a DNA test and further probe into the crime was underway, he said.