Mr Brown then sought to reassure the public over the crops some of which were planted this year and some in 1999.
Nick Brown told the Commons that he would make public any records of conversation that existed between his officials and the company, Advanta Seeds, to prove his point.
Conservative MPs said Advanta had been asked not to tell farmers about the planting of genetically modified oil seed rape.
The information was eventually made public one month after Advanta had told the government about the mix up.
Opening the debate, the Tory Agriculture spokesman Tim Yeo said Advanta had told him that they would have liked to warn their customers about the contaminated oil seed rape.
Secret
"The only reason they did not do so is that they were asked by Ministry of Agriculture officials to keep the whole matter secret."
"It was the Ministry of Agriculture's advice to Advanta and nothing else which ensured farmers were kept in the dark ... and allowed farmers to go on planting GM seeds in Britain after 17 April," he said.
Mr Brown intervened, insisting: "They had no advice from government not to tell their customers what had happened."
Mr Brown then rounded on Mr Yeo.
"Swampy"
"I invite the House to take a very hard look at the latest eco-warrior in front of us, the Swampy of south Suffolk - he has tried to present himself as a green consumerist concerned only to discover the facts," he said.
Mr Brown then sought to reassure the public over the crops some of which were planted this year and some in 1999.
"There is no risk to public health in this accident. There is no risk to the environment in this accident."
Joining the debate for the Liberal Democrats, David Heath, said his party had been disappointed in Mr Brown's handling of the affair.
"There was such a delay in making matters available to the public ear that there has been an impression given, if not a reality, of incompetence."
Turning to the minister Mr Heath said: "That is a serious charge against the Department and it will tell against your reputation."
At the end of the debate the Conservative attack on Labour's 'mishandling' of the issue was defeated by 267 votes to 144, a government majority 123.