Additional Chief Secretary K P Bakshi told reporters at a hurriedly-called press conference that all the cases against 55-year old Rajan, who has been deported from Indonesia, are being transferred to CBI because of its expertise in "handling transnational crimes".
Though there was no official word on it, sources said the underworld don who had fled the country 27 years ago had struck a deal with central security agencies under which all cases against him would be taken out of Maharashtra Police and that he would be lodged outside the state.
Mumbai Police has nearly 70 cases registered against Rajan, including 20 of murder, four cases under the Terrorist and Disruptive Activities (Prevention) Act, one under Prevention of Terrorism Act and over 20 cases under the stringent Maharashtra Control of Organised Crime Act.
Delhi Police has six cases registered against Rajan, who was a close aide of fugitive underworld don Dawood Ibrahim at one point but split before the 1993 Mumbai blasts were conspired.
In 2000, there was an attempt on Rajan's life when Dawood's men tracked him down to a hotel in Bangkok but he managed a dramatic escape by jumping from the first floor of the hotel.
Rajan lands in India on Friday, 27 years after he had fled the country in the face of numerous cases of murder, extortion and drug smuggling against him.
His deportation was deferred as the international airport in Bali was shut down due to spewing of volcanic ash from a nearby mountain.
After the authorities declared the airport open, the Indian team comprising CBI, Delhi and Mumbai police officials began the process of deportation of Rajan, who had fled India in 1988 for Dubai.
Sources privy to the developments said the underworld don, who was arrested on October 25 after the Australian police tipped off the Bali police about his presence in the island, was to undergo mandatory health check up before he would emplane a special aircraft for Delhi.
India was keen that the deportation takes place at the earliest and had put in a request to Indonesian authorities immediately after his arrest, the sources said.
Rajan, whose real name is Rajendra Sadashiv Nikalje, is wanted in over 75 crimes ranging from murder, extortion to smuggling and drug trafficking.
'J Dey murder case priority when Rajan is brought to Mumbai'
The case related to the murder of journalist Jyotirmoy Dey will be given priority after Rajan is brought to the city and may be reinvestigated if court orders for it, Mumbai Police Commissioner Ahmed Javed said.
"Dey's murder case is on trial before court. Police cannot reopen the case independently. If court orders reinvestigation, Mumbai Police is duty bound to do so as an investigation agency," he said.
Dey, a journalist with a local tabloid, was shot dead by motorcycle-borne sharpshooters on June 11, 2011. He had done many reports on underworld dons Dawood Ibrahim and Rajan.