Talks on Monday between Donald Rumsfeld and Cho Young-kil were aimed to build a consensus on security issues concerning Iraq, North Korea and troop deployments.
But protests were so fierce on Monday that Rumsfeld was forced to enter the ministry building through a side gate with the South Korean minister.
Dozens of demonstrators denounced requests for additional troops for Iraq.
"No blood for Bush," read a placard held up by the protesters who used loudspeakers to shout slogans denouncing South Korea's decision to dispatch troops to Iraq.
Some even hurled eggs at a portrait of the crossed-out US defence secretary, chanting "Rumsfeld, Go Home!"
"Don't make our young men the bullet shields of the United States," they shouted towards the museum across the street.
South Korean activists opposed President Roh Moo-Hyun's decision last week to dispatch 3000 non-combat troops to Iraq.
Roh's plan fell short of Rumsfeld's reported demand for more than 5000 soldiers to support US-led occupation forces.
But presidential security adviser Ra Jon-Yil said before the security meeting: "Our stance has been set. The United States seems to be accepting our position."
Protests began when Rumsfeld
inspected the guard of honour
The troop dispatch is politically sensitive in South Korea, split between opponents and supporters of Roh's decision, and has been condemned as a "criminal act" by North Korea.
Rumsfeld's first visit to Seoul as President George Bush's defence secretary comes as diplomatic efforts intensify to bring North Korea to a new round of six-way talks aimed at ending the year-long nuclear crisis.
A South Korean official indicated on Monday that a new round of talks could be held on 17 December in China.
The two Koreas, China, Japan, Russia and the US held an inconclusive first round in Beijing in August.
Meanwhile, Washington is proposing pulling back about 15,000 troops of the 2nd Infantry Division from the frontline with North Korea to bases south of Seoul.
The relocation is part of a realignment of US troops in Asia. Washington has also suggested consolidating or repositioning US bases in South Korea.
America has about 37,000 troops in South Korea who, alongside with 700,000 South Korean troops, serve as a deterrent against North Korea's 1.1 million strong army.
But Rumsfeld believes it can deter North Korea more effectively with long-distance precision firepower and at the same time lighten the ground presence that has been the source of political controversy in South Korea.
Analysts say the consolidation of US forces could lead to reductions in overall troop numbers in South Korea.