The remains were found buried little away from a Homoeopathic college run by a local politician. The complex also houses a higher secondary school and an engineering college, Ponda police who are investigating the case said.
The skeletons have been sent for forensic examination to the state-run Goa Medical College and Hospital.
Police said they would be able to know the gender, age and other details only after getting forensic report.
"The foul play cannot be ruled out because we have found nine skeletons in one pit," police said.