The accused were caught while attempting to dispose of the clerk's body in a neighbouring district, they added.
The deceased, Rahul Kumar Pandey, was a clerk at Madhavanand Inter College in Kasela village under Jaitra police station limits.
Jaitra Station House Officer (SHO) Ritesh Thakur said the car driven by the accused was intercepted in the Patiali police station area of neighbouring Kasganj district after receiving information about the murder.
"During the search of the vehicle, Rahul Kumar Pandey's body was recovered from the boot of the car. The college principal, Krishna Kumar Pandey, and another person travelling in the vehicle were arrested on the spot," the SHO said.
According to police, preliminary investigation suggested that an ongoing dispute over administrative supremacy and management of the college could be the motive behind the murder.
The victim's family alleged that Pandey was called to the college on Sunday, where he was murdered as part of a pre-planned conspiracy.
The body has been sent for post-mortem examination, the SHO said.
Thakur added that an FIR has been registered after a complaint by the victim's family.
Police are also probing the unidentified mobile number from which information about the incident was received, and further investigation into the case is underway, he said.
