Police detained 900 people, the BBC reported. The protests were led by South Korean farmers, who enjoy some of the world's largest subsidies.
While the demonstration raged outside, delegates inside the conference center were unable to agree on a date to end farm subsidies. The United States, joined by many of the poor countries, pushed for a 2010 target date, but the European Union refused to agree.
The draft text of a declaration for the meeting included no mention of a date.
The talks are scheduled to end Sunday with some of the delegates threatening to walk out before then.
"There is a need to inject political energy into the negotiations," Brazilian Foreign Minister Celso Amorim said, calling for a summit of world leaders.