The agency said there were no injuries reported in the violence in Taripa village, around 90 km (55 miles) from the coastal town of Poso, Authorities were not immediately available for comment.
According to the report, more than 100 local youths hurled rocks at the helicopter as it took off following a visit by the police chief. The chopper was apparently not damaged. The mob then torched three cars and a local police post.
Antara said the crowd was angry at the executions last week of three Christians for their part in attacks on Muslims six years ago during a war between the two faiths that left more than 1,000 people from both sides dead.
The executions sparked riots last week on the Christian-majority island of Flores, the birthplace of the three militants, but Sulawesi itself did not see any violence amid a police crackdown.
Christians in overwhelmingly Muslim Indonesia have questioned the fairness of the trials and maintain the three men - the only people to be executed over their roles in the conflict - were made scapegoats.