The two were produced at the ACJM court at Barrackpore on Friday and remanded to judicial custody for 14 days.
Shukla, a close aide of Barrackpore MP Arjun Singh, was shot dead in Titagarh on October 4. The state Criminal Investigation Department is probing the case.
The delegation alleged the state CID, which is investigating the case, is misdirecting the probe to falsely implicate political opponents in the BJP, Dhankhar said in a Twitter post.
The petitioner claimed that acts of the West Bengal government and its police in investigating Shukla's death have eroded the confidence of the common man in the law and order machinery of the state.
One of the accused had a rivalry with Shukla since his father’s murder in 2015, said the CID.
The two were picked up on Monday night from their residences in the district, a senior police officer said on Tuesday.
Senior TMC leader and Minister Firhad Hakim said Shukla was forced to join the saffron party last year by BJP MP Arjun Singh.
Manish Shukla, BJP leader and councillor of Titagarh Municipality in North 24 Parganas district, was shot dead by unidentified miscreants Sunday night in the area.
The police, however, said the saffron party was denied permission to take the body to the Governor House.
TMC said the incident was a fallout of the saffron camp’s internal feud. Shukla was a member of BJP’s Barrackpore organisational district committee.
Two bike-borne assailants opened fire at Manish Sukla on B T Road in the evening, following which he was taken to a private hospital, police said.