The children, identified as Asma (8), Aliba (7) and Abdullah (8), had gone missing from outside their house on Friday evening.
Police said that the three children were playing outside on Friday evening when they suddenly went missing.
Their family members, who began a search and informed the police at Bulandshahr police station, claimed that police did not register an FIR even after a written complaint was given to them.
On Saturday morning, the bodies of all three children were found in Dhaturi village, around 15 km from the spot where they were last seen.
The bodies have been sent for a post-mortem examination and a police investigation is underway.
Bulandshahr's Senior Superintendent of Police N. Kolanchi said that the families of the dead children are related to each other and police suspect family enmity to be the reason behind the brutal killings.
However, he also admitted to lapses in police action and ordered the suspension of Nagar Kotwali SHO and his assistant.
"We have constituted four teams to nab the prime accused Salman Malik in the case. The SHO of Nagar Kotwali and his 'munshi' have been suspended for the lapse. If they are found guilty, they will face a departmental probe. Our priority is to nab the culprit at the moment," Kolanchi said.
The sensational triple murder has led to anger and tension in the area.
( With inputs from IANS )