The airport resumed its activities at around 12.00 a.m. after the aircraft was towed away from the scene, he said.
"The airport's operations have returned to normal," he said.
No injuries or casualties were reported in the accident.
The cargo aircraft, with four crew members aboard, carried 16 tons of goods. It overshot Runway 30 as it experienced disruption when it was about to take off.
The B 737-300 aircraft bearing register number PK-YSG had originally planned to fly to Wamen City in Papua Province.
Related news: Trigana cargo aircraft overshoots runway at Sentani Airport
Related news: 700 security personnel secure Jayapura's Sentani area: police