The suitcase was found dumped near a well-known marine training institute on Palm Beach Road in Nerul.
The deceased seemed to be in her 20s, a senior police official said, adding the head of the woman was also found in the suitcase.
The body has been sent for postmortem.
NRI Coastal Police have register a case under sections 302 (punishment for murder) and 201 (causing disappearance of evidence of offence) against unidentified person(s), the official said, adding that further investigation is on in the matter.
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"Based on a missing person complaint, which was registered at the MIDC police station in suburban Andheri yesterday, we have identified the deceased as Shardabai Khotkar," said DCP (Zone XII) Vinay Kumar Rathod.
He said the Aarey Colony police have registered a case of murder against unidentified persons as the body bore injury marks.
Further investigation is on, the officer said.