MSPs have voted by a majority of just one to back a Scottish Executive decision to allow the commercial growing of GM crops in Scotland.
Scottish ministers say they want to set up GM-free zones
The Scottish National Party had tried to block the planting of GM maize until a full inquiry had been held.
But their motion calling for a delay was defeated on Thursday by 60 votes to 59.
The SNP blamed the Scottish Liberal Democrats for the result, accusing them of a climbdown.
The party's environment spokeswoman Roseanna Cunningham said: "The Lib Dems have abandoned their principles and opened the door to GM.
"This flies in the face of the wishes of the majority of Scots and of their own party policy.
"The ban on GM maize failed by just one single vote. If just one Lib Dem had found the backbone to stand by their own policy, the executive would have been told Scotland must remain GM free."
"The party has proved they are totally spineless and unable to stand up for what they claim to believe.
"On vote after vote they back the Labour Party over the Scottish interest, ignoring the Scottish interest. They should be ashamed."
Earlier on Thursday Deputy Environment Minister Allan Wilson accused the SNP of jumping on "a passing bandwagon", insisting the executive had no legal basis to refuse consent for Chardon LL maize because there was no scientific evidence that the crop presented any health or environmental risks.
Mr Wilson insisted the decision to permit the crop to be grown had followed the "most thorough examination of the science" and in the absence of "credible scientific evidence of potential harm" a ban would be illegal.
Despite giving their backing to the Westminster plans last week, Scottish ministers have said they would help create GM-free zones in some parts of the country.
The executive has also stressed it is planning legislation to govern how GM farmers could live side-by-side with conventional and organic growers.
Tory rural development spokesman Alex Johnstone said ministers had failed to adequately justify their decision to the public.
He also said the issue of liability had yet to be resolved, while the executive had given no details of how the voluntary GM-free zones would operate.
Lib Dem environment spokeswoman Nora Radcliffe said the executive was acting within the law and urged opposition parties to unite behind the executive's efforts to encourage a voluntary GM-free zone.
But Mark Ruskell, the Green's environment spokesman, claimed the executive's approach to the precautionary principle was "upside down".
He said: "The field scale evaluations were very narrow and didn't deal with the issue of contamination at all.
"Until we see the executive's legal advice we'll treat the reassurances on the precautionary principle as the 'waffle a lot and hope for the best' principle."