The clash occurred on Tuesday when 1500 to 2000 farmers gathered in southern Kandahar province's Maiwand district to demonstrate against the counter-narcotics team.
The team was on an eradication mission, Muhammad Nahim, deputy head of intelligence in Kandahar, said.
The protesters had blocked the main highway between Kandahar and Herat, the main city in western Afghanistan.
"As the police, escorting the counter-narcotics force tried to push them back, some of the farmers tried to attack the police who then fired on the crowd in self-defence," the official added.
An Afghan intelligence source said at least 600 members of the US-backed poppy eradication force had been sent from Kabul.
Their job is to tackle burgeoning opium production in the province, which has risen since the beginning of the year, according to the UN.
Farmers say they were given no
time to plant alternative crops
Witnesses said the road had been blocked with burning tyres and US helicopter gunships were circling above the surging crowd.
The farmers were complaining that the authorities had waited too long to start wiping out their poppies and now they would have no time to plant alternative crops, a Western security source said.
Intelligence official Nahim and Kandahar police chief Muhammad Ayub Salangi both said US helicopters were flying over the crowds.
"We know that there were some American helicopters, but we didn't know if they were involved in the clashes," Nahim added.