Police said the locals were killed as the security men had to fire at them in a retaliatory action after the villagers took the policemen in hostage for hours.
Those killed are identified as Jhoti Sah of Bauratar-8, China Sah (17) and Raj Kumar Patel of Hariharpur, police said.
A police team led by Inspector Madan Jha from APF Base Camp at Titrauna reached the village in suspicion of storing arms and ammunition inside a house. But the locals confined them inside a building for hours in suspicion that they might be robbers.
The locals were shot dead after the APF personnel came outside the building after breaking the building doors.
DSP Rajendra Basnet of APF in the district claimed that the policemen had to open fire only after the locals started setting fire to the security personnel inside the building.
However, the locals claimed that they took the police, who were in civil dress, into their control with a plan to hand them over to the police thinking that they might be looters. Locals said the policemen fired indiscriminately at the villagers.
Those injured are undergoing at Narayani Sub-regional Hospital in Birgunj.
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