Among those detained include the assistant to the district commandant, identified as Satish, and two home guards constables, identified as Anil and Pinku Kumar.
The fire, which occured in the early hours of Tuesday, destroyed salary muster rolls of personnel dating back to 2014. Last week, the state government had ordered a probe into the alleged scam relating to fake attendance of home guards and withdrawal of money by fraudulent means.
According to the police, Anil was sleeping in the front room of the office as he was the night guard. Anil told the police that during the early hours of Tuesday, when he woke up to use the restroom, he realised that the door to his room was locked from outside.
Anil told police that the sweeper who had come to clean the premises unlocked Anil's door in the morning. He was then told about the fire in the room where the attendance logs of the home guards personnel were kept.
Senior Superintendent of Police (SSP) Vaibhav Krishna said: "We have detained three persons for questioning. Satish has been detained as he is the senior most officer in the home guards department. Anil was detained as he was the only person present on the premises when the fire broke out. Pinku has detained on suspicion."
Tanu Upadhayay, circle officer (CO), Greater Noida 1, said that officials are unaware of the exact timing of the fire, but it possibly broke out in the early hours of Tuesday.
"We could not find any CCTV camera in or around the district commandant's office. Our investigation is on in the matter and the persons behind the incident will be arrested soon," the CO said.
Krishna said the perpetrators broke the lock of the room where the attendance logs were kept and also the two locks which were put on the box containing the logs.
The fire did not attract immediate attention as the smoke escaped through the windows that open towards the rear of the building.
The police have sealed the room where the documents were burnt as well as two adjacent rooms.
A forensic team from Gautam Budha Nagar visited the spot Tuesday afternoon on the orders of Chief Minister Yogi Adityanath.
Jitendra Kumar, Station House Officer, Surajpur police station, said that forensic teams from other states have also been called in because burning of the logs clearly indicates that some people are scared of the investigation into the Rs 7.5 lakh fraud case related to the home guards' salaries.
( With inputs from IANS )