The surprise verdict acquitted the seven men of conspiracy and firearms offences.
A lawyer for Ammon Bundy was tackled to the ground by marshals after shouting at the judge.
The militia occupied the refuge in early January, accusing the government of unlawful interference in the affairs of ranchers.
One protester was shot dead by police during a confrontation outside the refuge when some of the defendants were arrested, days before the occupation was brought to a peaceful end in February.
The stand-off highlighted the simmering resentment among rural communities in the West over federal control of land.
A total of 26 people have been charged over the stand-off. Some have already pleaded guilty to conspiracy.
A second group of defendants is due to stand trial in February.
Prosecutors argued the defendants, led by Ammon Bundy and his brother Ryan, had kept federal employees from their jobs at the Malheur National Wildlife Refuge.
However, defense lawyers say the jury was unable to find beyond reasonable doubt that the occupiers had intended to prevent federal officers from going to work.
Drama erupted in the courtroom after Ammon Bundy’s defense lawyer Marcus Mumford shouted at the judge, demanding the immediate release of his client. As the exchange escalated, court marshals tackled him to the ground and used a stun gun on him.
Judge Anna Brown said Ammon Bundy could not be released because he and his brother still faced charges in a separate armed stand-off case at their father’s ranch in Nevada in 2014.
Lawyers for the defendants expressed their surprise at the verdict, including Robert Salisbury who described it as a “stunning victory for the defense”.
Alongside the Bundy brothers, Jeff Banta, Neil Wampler, Kenneth Medenbach, David Fry and Shawna Cox were all cleared of the charges.
During the occupation , the group established armed patrols and vetted those who visited the refuge. They said the takeover was a justified act of civil disobedience against an overreaching federal government.
After several weeks one of the protesters, Robert “LaVoy” Finicum, was shot dead during a 26 January traffic stop outside the refuge as the Bundy brothers and several others were detained.
After the acquittals, US Attorney for the District of Oregon Billy Williams said he had “hoped for a different outcome”.
However, he said he strongly believed the case needed to be brought before a court and decided by a jury.
The FBI also said it was “extremely disappointed in the verdict”.
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