Prabhakar, a 2003-batch IPS officer who was Deputy Commissioner of Police (East), was transfered to Prime Minister's Security in the same rank, a senior police official said.
Prabhakar had headed the district where the rape of the five-year-old girl in Gandhinagar led to protests in the capital.
It was alleged the local police did not investigate the kidnapping and subsequent rape of the girl properly. A Vigilance Enquiry had indicted the Station House Officer of Gandhi nagar Police for dereliction of duty.
Chhaya Sharma, a 1999-batch officer who was heading South Delhi district as its Deputy Commissioner of Police, was transfered to Mizoram. DCP (Outer) B S Jaiswal, a 2001 batch officer, replaces her.
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Sharma had headed the South district when the gangrape of a 23-year-old woman in a moving bus on December 16 last year, took place.
A senior police official said the transfer of Prabhakar came against the backdrop of the rape incident and it was "obvious".
On Sharma's transfer, the official said AGMU cadre officers have to serve outside Delhi also and her posting to Mizoram was due.