The pastor's close friend, Pastor Peter Aricha, praised the late Mr Kibagendi, describing him as a man dedicated to serving God and humanity.
His disappearance attracted the attention of the national Adventist church, with officials calling for anyone with information that could lead to his whereabouts to come forward.
He said they had suspected foul play in his disappearance and news of his body only confirmed their fears.
Pastor Kibagendi is believed to have been lured by an unknown caller from his Kijauri home before he walked out onto the tarmac and disappeared.
Area chief Mike Onsombi said the pastor was last seen making a phone call near Riensune Primary School.
“He was found near the school and we are wondering who are behind the cold murder,” he said.
His widow, Jenniffer Kibagendi, said her husband was in a jovial mood on the day he went missing and had breakfast with the family.
“We only suspected that something was amiss when his phones went off at noon and he had not returned home," she said.
She said they had been attacked by thugs three times since they moved to the region a decade ago but did not suspect any possible connection between those attacks and the latest incident.
They have five children.
Borabu police boss Anthony Onyango said they are treating the case as a murder.
“Three weeks ago, we started investigations after it was reported to us that the pastor was missing. But we now treat this as a murder case and we promise to bring his perpetrators to book,” he said.
In early April, in the same area, a police officer identified as a Mr Odero went missing before his body was found 10 days later dumped near a river.
The two cases have left residents in shock, but police say the two deaths are not related.
A local leader, Alephaxard Osoro, called on police to ensure the killers are arrested and prosecuted.
“We feel that we are no longer safe. Police should ensure our security,” he said.