Crop trials have sparked fierce debate in Scotland
More than 100 protesters turned up at Tullich Farm near Munlochy on the Black Isle.
About 12 entered the field and a land rover was driven through a section of the GM oilseed rape.
The three men are due to appear at Dingwall Sheriff Court on Tuesday in connection with the incident.
The crop trials have been the target for months of sustained attacks by protesters.
Thousands of people, including local MPs and all non-ministerial MSPs from the Highlands, have backed the call for a halt to GM experiments on farms.
Scottish National Party leader John Swinney has accused ministers of treating Scotland as a "live laboratory" by permitting the field trials.
And the Scottish Parliament's transport and environment committee has also urged the Scottish Executive to plough up the oilseed rape crop.
The committee's call was made despite assurances in a letter to MSPs from the Environment Minister Ross Finnie that there is no new evidence the trial poses any harm.
Impact of environment
Mr Finnie also said he was bound by a European directive to allow the test to continue.
Dr Eleanor Scott, of the Scottish Green Party, said many people had devoted a large part of the past year to keeping the Highlands GM-free.
If the executive continued to ignore them, she said, more direct action was inevitable.
Five demonstrators appeared at Dingwall Sheriff Court a week ago and admitted destroying oilseed rape GM crops at the farm.
Twelve trials have taken place in Scotland and the final planting of GM seeds is scheduled to take place next year.
Concerns surrounding GM technology centre on the impact on the environment, wildlife and human health.