Special Judge Anupam Srivastava issued the warrants against Sultan Masood, father of Shehla, and family relative Sayyed Rahil Hussain, senior public prosecutor Hemant Shukla told reporters here.
The next date of their (witnesses) deposition would be fixed tomorrow, Shukla said.
The court also asked the CBI to take responsibility for producing its witnesses in court, to avoid further action against them.
Defence lawyers Sunil Srivastava and Pervez Alam urged the court to issue warrant against the absent witnesses.
Two new witnesses, Sohail Athar Zaidi and M R Uikey, will appear before the court tomorrow.
Shehla was shot dead outside her house in Bhopal on August 16, 2011.