Two people were killed in the southern Philippines after clashes between police and thousands of drought-hit farmers protesting over a lack of food, a demonstration leader said Saturday.

Patches of blood stained a parched highway in impoverished Kidapawan city, capital of Cotabato province, which had been barricaded by 6,000 farmers since Wednesday to demand 15,000 sacks of rice from the government.

Gunshots were fired and rocks hurled into the air during a scuffle between police and demonstrators on Friday, an AFP photographer on the scene saw, as the authorities tried to disperse the crowds.

"We asked for rice. Instead, they gave us bullets," protest leader Norma Capuyan, who witnessed the melee, told AFP.

"The farmers are starving because they have nothing to eat. We went there looking for a solution."

The Philippines has been gripped by a strong El Nino dry spell since December which has hit food production, particularly in the conflict-wracked south which is home to the country's poorest and where more than half of the population is reliant on agriculture.

Panicked protesters picked their bloodied comrades from the highway and treated their wounds by the roadside as they were sprayed with water from firetrucks, Capuyan said.

"Everyone was angry. The police were hitting us. It was a real commotion," Capuyan said, adding that the rallyists had left the highway and retreated to a nearby church.

Capuyan claimed 116 protesters were wounded while 89 others were missing. The two gunshot fatalities were male farmers in their 40s, she said.

Police could not immediately confirm the fatalities, but said 40 of its men were also hurt in the ruckus, two of them in critical condition.

Authorities "exhausted all possible remedies" to end the protest peacefully, but farmers started the scuffle by throwing rocks and twigs, national police spokesman Chief Superintendent Wilben Mayor said in a statement.

North Cotabato governor Emmylou Mendoza told reporters she was taking "full responsibility" for the incident.

Presidential spokesman Manolo Quezon said an investigation was underway.

"There is no reason why people must die for asking for assistance from their own government," he told reporters on Saturday.

The state weather bureau had warned last year that rainfall could decrease by as much as 80 percent during the drought, which is expected to last until the middle of this year.