Many protesters are demonstrating against the presence of US President George W Bush and his free trade agenda.
Riot police fired tear gas to disperse demonstrators wearing ski masks and scarves who were throwing stones and Molotov cocktails at security forces around 600 metres from the hotel where leaders from 34 countries in the Americas are meeting.
About 300 demonstrators were involved in the clashes, with around 8,000 security forces deployed to the resort in anticipation of protests.
Earlier, more than 10,000 people peacefully demonstrated in an anti-US protest led by Argentine football hero Diego Maradona.
Other prominent protestors included Nobel Peace laureate Adolfo Perez Esquivel and the populist frontrunner in Bolivia's presidential race, Evo Morales.
The peaceful demonstrators gathered in a stadium, where the crowd grew to 40,000 people and included leftist Venezuelan President Hugo Chavez, an outspoken critic of Mr Bush.
Demonstrators set American flags on fire, while others used slingshots to fire rocks at police.
Several shops had their windows shattered during the rioting and at least one building was set on fire, according to a CNN report.
Chavez makes anti-FTA speech
Earlier, President Chavez urged protesters to help him "bury" the FTAA.
He said the planet "is being destroyed under our own noses by the capitalist model, the destructive engine of development", adding that "every day there is more hunger, more misery thanks to the neo-liberal, capitalist model".
The Venezuelan leader is a leftist ally of Cuba's President Fidel Castro, the only leader in the Americas not invited to the summit.
He also vowed a "100-year" war if the US ever invades Venezuela -- something he has repeatedly accused the American government of planning, although US officials deny any such plans.
The protest also featured Argentine soccer great Diego Maradona, clad in a "Stop Bush" t-shirt, and Bolivian presidential hopeful Evo Morales, both of whom travelled to Mar del Plata aboard an overnight train packed with protesters chanting "Fascist Bush! You are the terrorist!"
Mr Bush acknowledged the tensions during a meeting with Argentine President Nestor Kirchner.
"It's not easy to host all these countries. It's particularly not easy to host... perhaps me," he said.
He has vowed to be polite if he speaks with Mr Chavez, with fears that any confrontation between the two leaders might overshadow the summit.
Opposition to free trade
Mr Bush is hoping to revive talks aimed at uniting the region in a Free Trade Area of the Americas that would stretch from Canada to Chile, but exclude Cuba.
He argues that all nations will benefit economically.
But the US leader is facing opposition, and there has been no indication as yet that any compromise has been reached.
The summit nations failed to agree on a declaration that would have backed the proposed free trade area.
Instead, ministers adopted a compromise calling for a renewed focus on addressing poverty and unemployment.
Brazil's Foreign Minister Celso Amorim confirmed that his country, along with Argentina, Uruguay and Paraguay, oppose fixing a date to resume negotiations on the FTAA.
The US, Mexico, Canada and Central American governments want talks on the project to resume in 2006.
Opponents argue that US-backed free market policies have pushed millions in the region into poverty.
But supporters of free trade say those policies are not to blame for the region's problems and argue that the pact would promote growth and boost the region's economies.
The summit also sparked demonstrations in Venezuela and in the Argentine capital of Buenos Aires and Caracas in Venezuela.
Canada and the US are among the richest countries in the world, while almost half of Latin America's 512 million residents live in poverty.
The United Nations says around 96 million people in the region survive on less than a dollar a day.