The two were reported missing since Friday.
The bodies -- bearing injuries, hands and feet tied, wrapped in plastic sheets and packed tight in cardboard boxes - were dumped in a drain in Kandivali suburb.
"It is a clear case of murder. We will find out the cause of injuries only after the postmortem report comes out," said senior Mumbai police officer Vikram Deshmane.
The Mumbai Police are questioning Hema's estranged husband, artist Chintan Upadhyay - against whom she had filed a harassment case -- and her domestic helps. Harsh Bhambani, 65, was representing her in the case.
Ms Upadhyay, 43, had got married to Chintan Upadhyay in 1998. In 2010, they had filed for divorce.
The harassment case was filed two years ago. In her complaint to the police, Ms Upadhyay had accused Chintan Upadhyay of painting obscene sketches on the walls of her room in their Mumbai apartment.
A well-known artist, Ms Upadhyay had won awards from the Gujarat Lalit Kala Academy and the national Lalit Kala Academy.
She used photography and sculptural installations to explore personal identity, dislocation, nostalgia and gender.
Her works have been displayed at various international exhibitions -- in China, Australia, France, Israel and Japan.
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