The protesters, mostly women belonging to Brazil's branch of the international Via Campesina farm workers rights group, occupied the plantation about 1200 km south of Sao Paulo before dawn.
Via Campesina said it organised the invasion "to denounce the social and environmental impact of the growing green desert created by eucalyptus monoculture" in Latin America's largest country.
They overpowered security guards and left after causing damage, Aracruz Papel e Celulose SA said in a statement.
Irma Ostroski, a co-ordinator, said: "We don't want the green desert of the cellulose firms. We want a country that produces food."
Lab equipment destroyed
Aracruz said the demonstrators destroyed saplings and laboratory equipment. Renato Rostirolla, the company's regional orchard director, said: "They smashed up the heart of the farm."
The damage included the loss of 20% of the saplings ready for planting - about a million plants.
"The laboratory was completely destroyed, especially seeds and tests, and broken computers," he said.
The lost tests included 15 years' worth of genetic research. Actual damage was about $400,000 but the intangible losses ran to millions of dollars, Aracruz claimed.
In a manifesto published on Via Campesina's website, the group said that increasing cultivation of eucalyptus and other trees to make paper and pulp across the region is forcing poor farmers from their land, causing pollution and creating health problems.
"We are against green deserts, the enormous plantations of eucalyptus, acacia and pines for cellulose, that cover thousands of hectares in Brazil and Latin America," the statement said.
"When the green desert advances, biodiversity is destroyed, soils deteriorate, rivers dry up. Moreover cellulose plants pollute air and water and threaten human health"
Via Campesina, farm workers rights group
"When the green desert advances, biodiversity is destroyed, soils deteriorate, rivers dry up. Moreover, cellulose plants pollute air and water and threaten human health."
The company said: "Aracruz repudiates these acts of vandalism, intimidation and invasion of private property, which it considers an affront to democratic principles and the rule of law."
Miguel Rossetto, the agricultural development minister, condemned the action in a statement from Brasilia.
Antonio Hohlfeldt, the state governor, said police had video of the damage and intended to investigate those responsible.
Via Campesina, on its website, did not mention any damage.
When asked by Reuters, Ostroski said the protesters staged a "symbolic action" of destroying saplings. "As we were more than 2000 women, it's impossible to say how far people went," she said.
The demonstrators later marched to Porto Alegre to protest at a United Nations conference on agrarian reform.
Small farmers and environmentalists say they fear a rapid expansion of planting in the area by Aracruz, which is studying increasing production at its cellulose unit in the state.
Via Campesina is an international peasants' organisation linked in Brazil to the MST (Landless Peasants Movement), which often invades large farms.
Wednesday's raid was timed to coincide with International Women's Day.