Senior Judicial Magistrate MM Morshed passed the order following a petition filed by sub-inspector Sumon Quaderi of Kushtia Model Police Station, also the investigation officer of the case.
Presenting the evidence before the court that the bus owner and driver were responsible for the accident, the IO prayed to it for cancelling their bail.
Later, the court issued the arrest warrants cancelling their bail.
Earlier on Monday, MM Morshed granted bail to bus owner Joynal Abedin and driver Mahid Miah alias Khokon in the case.
Members of Rapid Action Battalion (Rab) in a drive arrested Joynal Abedin from his house in Faridpur district town on Sunday.
Besides, Khokon surrendered before the court on Monday morning.
Akifa, a one-year-old daughter of Haruur Rashid, who sustained injuries after she fell from her mother Rina Akter's lap when a bus of 'Ganj-e-raj Paribahan' hit the mother in Kushtia district town on August 28, died at Dhaka Medical College Hospital (DMCH) in the capital on August 30.
The victim’s father filed a case against bus driver Khokon, its owner Joynul and supervisor Yunus with Kushita Model Police Station on the same day.
The video footage of the incident went viral on social networking site Facebook, sparking uproar across the country.