"It is just a rumor," Merpati General Manager for Papua David said.
Merpati did not serve a Jayapura-Oksibil route, he said adding only Trigana and Pelita Air served the route.
A report had it that a Merpati Twin Otter plane carrying 13 people including two infants lost contact with the control tower on Sunday.
The report said the fate of all people aboard the plane was still unknown.
Reporting by Hendrina Dian Kandipi