Thirteen people, including a senior military commander, were killed when an Indonesian military chopper taking part in an anti-terror operation crashed.

The military helicopter crashed on Sunday evening in the Poso regency of Central Sulawesi, killing everyone on board.

"The helicopter is believed to have been hit by lightning before it crashed. Weather has been bad in the area over the last couple of days," a senior official said, according to Jakarta Post.

The chopper was participating in an anti-terror operation targeting the East Indonesia Mujahidin (MIT) terror group.

Poso Police chief Ronny Suseno said the victims included Tadulako military commander Col. Saiful Anwar who was also deputy chief of Operation Tinombala. The chopper crashed at 6:20 pm local time in Pattiro Bajo hamlet, South Poso Pesisir district.

Security officials said that despite the mishap, the operation against a key figure in the MIT leadership was on course.

They said they would soon arrest MIT leader Santoso, known as Abu Wardah, one of the country's most-wanted men.

The operation against Santoso is related to the killing of two Uyghur's last week in police encounter.

"I'm speechless. I express my deepest condolences. The price of this terrorist hunt is too high," Central Sulawesi Governor Longki Djanggola said.