The two officials are at present under suspension.
The accused will be produced before the competent court on Thursday, they said.
The two have been arrested over allegations of criminal conspiracy and destruction of evidence, the officials said.
The rape survivor had alleged that she was raped by the MLA at his residence on June 4, 2017 where she had gone with a relative seeking a job.
The survivor's father was booked by the police under the Arms Act on April 3 this year and put in jail on April 5.
Frustrated with the alleged inaction and coercion from powerful people, the survivor attempted self immolation in front of Uttar Pradesh Chief Minister Yogi Adityanath's residence on April 8.
The next day, her father died in jail, with the postmortem report mentioning serious injuries on his body.