Additional Chief Judicial Magistrate AFM Ahsanul Haque issued the warrants on Thursday, said court police's Inspector Abu Sayeed Sarkar.
The three who are still on the run are Rajibul Islam Badal alias 'Badhan', Abdul Khalek alias 'Khaled' alias 'Mama' and 'Rajib' alias 'Sujan' alias 'Jakir'.
Sarkar told bdnews24.com that the case investigation officer, Detective Branch's Sub-Inspector Bazlur Rashid, submitted the chargesheet on June 30.
Motorcycle-riding assailants shot Italian priest Piero Parolari, 78, in Dinajpur town in the morning of Nov 18, 2015, when he was on his way to the St Vincent Hospital, where he worked. He was hit on the neck.
The missionary was rushed to Dinajpur Medical College Hospital in critical condition where doctors operated on his neck. He was later sent to Dhaka for better treatment.
After recovering, Parolari returned to Italy.
The case over the attempt to murder Parolari was later started at Kotwali Police Staion.
Police have already arrested four of the seven accused.
They are Shariful Islam alias 'Denis', Sakhawat Hossain alias 'Shafiq Master', Sarwar Hossain alias 'Sabu' alias 'Mizan' and Abdur Rahman alias 'Pintu' alias 'Badshah'.
Source: Bangladesh's First Internet Newspaper