Shaikh was attacked and killed near his home in Bankar Colony, Hadapsar following violent protesters to the presence of derogatory contents of Shivaji Maharaj and late Shiv Sena Chief Bal Thackeray on social networking sites.
Following which, violent protests had broken out in parts of Hadapsar area on June 2.
A case of murder, rioting and criminal conspiracy has been registered with Hadapsar police and 19 youths arrested and remanded to police custody till June 12.
On Tuesday, Hadapsar police took Desai in custody for his provocative speech from Loni Kalbor police station which falls under Pune rural police. Desai has been charged with Shaikh's murder case under relevant section of Indian penal Code comprises of Criminal conspiracy.
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There are over 20 cases against Desai for making inflammatory speeches, circulating pamphlets against particular community and rioting, have been lodged against Desai with city police stations like Deccan Gymkhana, Shivajinagar, Cantonment police station, Hadapsar, Lonikand and several other police stations.
Joint Commissioner of police (Law and order) Sanjay Kumar said, "We have arrested Desai in the Hadapsar case for his involvement in the murder. Our team of officers are investigating the case."
Speaking to dna, an officer said, "From the arrested persons, the police have accquired clips audio and video of provocative speeches made by Desai. We suspect that his speeches are main reason why they were instigated to do such acts and the murder was a fall out of such provocation."
Desai will be produced before the court on Wednesday.