State BJP president Ravindra Chavan issued the directive after Choudhary's induction into the saffron party at an event in Palghar, invited criticism from various quarters.
The state government had earlier told the apex court that the Maharashtra Police has punished "delinquent" policemen for dereliction of duties in the alleged lynching incident and sought dismissal of pleas seeking a CBI probe.
The pleas sought a CBI or a court-monitored Special Investigation Team probe in the incident that took place in the Palghar district in April 2020.
A total of 201 persons were arrested in the infamous case, of which 57 have been granted bail.
The police in Maharashtra's Palghar district averted potential mob violence against two sadhus in a village after the residents mistook them as child-lifters, nearly three years after three persons were lynched in the district over similar suspicion, an official said on Tuesday.
The Palgarh Police arrested 110 people including nine juveniles, in connection with the lynching of three persons by the villagers, suspecting them as thieves
Terming the incident as unfortunate and a blot on humanity, Deshmukh in a Facebook address said this is not the time to play politics, and urged all to engage in collective efforts to defeat the deadly coronavirus.
Solicitor General Tushar Mehta, appearing for the Centre, said media reports suggest that chargesheets filed in the case comprises of more than 10,000 pages.
The Supreme Court on Wednesday asked Maharashtra Police to place on record the second supplementary charge sheet filed in the case related to alleged lynching of three people, including two seers, in Palghar district in April last year.
A bench of Justices Ashok Bhushan, S K Kaul and M R Shah said that 'with regard to this incident, this court has already taken cognisance. There is no question of multiplying the petitions one by one'.
The team probing the incident examined 808 suspects and 118 witnesses to collect strong evidence against the accused, the CID said in a release.