After a day of protests, Greenpeace Brazil, the Brazilian Green party and non-governmentel groups announced that they would seek to get the decision overturned in the courts.
The government was divided on the decision, which was suported by agriculture officials, who said they were anxious to keep abreast of the latest technological developments.
Opponents of GM foods were disappointed by the apparent u-turn by President Luiz Inacio Lula da Silva, whose Workers Party (PT) resisted GM crops when it was in opposition.
It was presented as a one-year emergency measure because farmers in Rio Grande do Sul state have for several years smuggled large quantities of GM soya seed across the Argentine border.
The government accepted that there was little prospect of forcing them to buy conventional seed when the planting season begins in the next two weeks.
The GM company Monsanto now stands to gain up to $100m ($62m) a year from farmers who have been growing its seed illegally.
It has invested more than $600m in setting up seed plants and buying Brazilian seed companies. It recently announced that it would start charging farmers royalties on this year's soya crop.
US producers have long complained that Brazil has had an unfair advantage because many of its farmers do not pay royalties for black-market GM soya.
The lifting of the planting ban was described by critics as a triumph for the company.
"Instead of enforcing the law, the authorities have allowed big farming interests to dictate their own terms," said Karin Silverwood-Cope, a coordinator for the NGP Campaign for a GM Free Brazil.
Bob Callanan, head of the American Soybean Association, which is fervently pro-GM, said: "We have long been frustrated by Brazil growing illegal GM seeds. This would be a step towards allowing Monsanto to collect the fees due to it and help to end the paper shuffle where EU countries bought Brazilian foods and pretended that it was not GM."