The Sentani area near the provincial capital Jayapura has been hit by torrential rain since Saturday that triggered the floods, said the official, Cory Simbolon.
At least nine houses and two bridges were damaged by the floods, national disaster agency spokesman Sutopo Purwo Nugroho said, adding that a search and rescue team has yet to reach all the affected areas.
“Waters have now receded, leaving mud, logs and other materials carried by the flash floods,” Nugroho said in a statement.
More than 120 residents were taking shelter at government offices after their homes were hit by the floods, he said.
Authorities, aided by the Red Cross and volunteers, were responding to help the displaced, Nugroho said.