Miss Honduras, Maria Jose Alvarado, and her sister, Sofia Trinidad Alvarado, were found dead in their hometown of Santa Barbara early Wednesday in a suspected crime of passion linking to Sofia's boyfriend.
Police recovered their bodies in a shallow grave along the banks of the local Aguagua River around dawn, Honduran daily La Prensa reported.
"We are 100 percent sure that it's them," the daily cited the officer in charge of the investigation, Leandro Osorio, as saying.
Director of the National Police, Ramon Sabillon, was also quoted as saying that "there was 95 percent certainty the bodies found ... belong to Miss Honduras and her sister."
Police arrested late Tuesday Sofia's boyfriend, Plutarco Antonio Ruiz, on charges of kidnapping and killing the two, the report said.
Police suspected that Ruiz shot dead the elder sister after seeing her dancing with "another person or something similar, " then shot Maria Jose and buried the bodies, Osorio said.
"We have the material author of this abominable act, Mr. Plutarco Ruiz. We have found the weapon and the vehicle used to transport the (women)," Osorio said.
According to Xinhua, police were led to the bodies by a local farmer who regularly passed the site and noticed "something strange" there on Saturday, daily El Heraldo said.
The sisters were reported missing on Sunday, three days after they went missing after attending a birthday party near Santa Barbara, a city located 200 km northwest of the capital.
Honduran officials issued arrest warrants for the owner of the venue hosting the birthday party, and his wife and daughter, on charges of covering up the crime, the daily La Tribuna reported. Police believe the women were killed at the venue and later buried by the river.
A fifth suspect, Aris Maldonado Mejia, is also in custody.
Maria Jose, 19, who was crowned Miss Honduras World 2014 in April after beating 18 other contestants to the top spot, was due to fly to London Wednesday to compete in the 2014 Miss World pageant. The official website of the pageant still lists Maria Jose as one of the contestant as of Wednesday.