Mazgaon Metropolitan Magistrate R K Malabade on Monday ordered the senior inspector of J J Marg police station to investigate the matter and report to the court by January 30, 2010.
Significantly, the court has also asked the police to register a First Information Report and find out how and when the jacket went missing.
Social activist Santosh Daundkar had filed a complaint alleging that Karkare was wearing a bullet-proof jacket when he was killed.
His body was taken to the JJ Hospital for post-mortem and since then the bullet-proof jacket is missing. He claimed that the bullet-proof vest was a vital piece of evidence in the backdrop of allegations that it was defective and had therefore led to Karkare's death by allowing bullets to pass through.
The complaint was filed in Mazgaon court as JJ Hospital is located in its jurisdiction limits.
The magistrate noted, "It is a complaint against some unknown accused and hence at this stage following the reply given under the Right to Information Act, 2005, by the police to Kavita, wife of the deceased Karkare, the court is of the opinion that prima facie this is a fit case to carry out investigation."
"After the FIR is lodged, the police would be armed with statutory powers to search, carry out seizures, summon witnesses or arrest offenders," said complainant's lawyer Y P Singh.
Earlier, Maharashtra Home Minister R R Patil had ordered the Mumbai Police Crime Branch to probe the missing jacket after Kavita Karkare brought the matter to his notice.
Kavita had learnt through a RTI that the bullet proof jacket was missing.
Union Home Minister P Chidambaram had also apologized to her over the issue of the missing jacket.
A public interest litigation has also been filed in the Bombay High Court seeking action against erring police officers for inducting defective bullet-proof jackets into the police force and asking for a probe by an independent agency into the matter.