The scuffles erupted on Tuesday when riot police blocked about 200 slogan-chanting protesters from marching close to the presidential compound in central Seoul.
Protesters shouting "Down with Roh Moo-Hyun" pushed and kicked police who pushed them back using plastic shields.
Similar scuffles erupted earlier in the day when hundreds of riot police erected a barricade with buses to block 500 activists and students from entering a military airport at the southern outskirts of Seoul.
Dozens of students unfolded a banner reading "Scrap S Korea-US alliance" on top of the police buses as their colleagues wrestled with riot police at the gate of the airport.
Police blocked protesters from
going near presidential compound
South Korea will start deploying 3000 troops to northern Iraq from August.
The contingent of mostly non-combatants will be the third largest in the US-led occupation troops in the war-torn country.
The beheading of Kim Sun-Il, a 33-year-old South Korean citizen by a group in Iraq in June, fuelled anti-war protests in Seoul, but the government vowed to push on with the troop dispatch.
South Korea already has 660 army engineers and medics operating in the southern Iraqi city of al-Nasiriya.