The child, Shyam Kumar, was brought to the Rajendra Institute of Medical Science (RIMS) on Sunday.
The cost of the CT scan is Rs 1,350 and his father,Santosh Kumar, had Rs 1,300. He requested the lab staff to conduct the scan despite the shortage of funds, the police said.
But Shyam was refused the scan. His father phoned a friend who rushed over with the extra money needed, but by then, the child had died.
More details are awaited.