"There are 13 military officers and preliminary reports said they were killed but we are still trying to verify this information," I Made Sutia, a local military spokesman, told AFP.
The Bell helicopter went down in Kasiguncu village in Poso district, central Sulawesi, where a radical Islamic group is waging a guerilla war against the government.
The Indonesian military has been hit with repeated aircraft accidents in recent years.
Last month, a small Super Tucano turboprop plane crashed into a densely populated area during a test flight, killing three people.
And last June, a Hercules C-130 crashed into a residential neighbourhood in Medan, the largest city on Sumatra island, killing 142 people and causing widespread destruction.