Dr Brown is accused of remaining inside a logging coupe in the Styx Valley on February 19.
The 79-year-old former Greens leader appeared briefly in Hobart Magistrates Court on Monday, entered a plea of not guilty and had his bail continued.
Fellow activist Colette Harmsen also pleaded not guilty to one count of trespassing from the same protest.
The pair will next appear in court on July 5 ahead of an expected hearing.
"We've pleaded not guilty because we're not guilty," Dr Brown said outside court, accusing Tasmania's major parties of backing "outrageous misuse" of state forests.
"We've got government backing a job-losing industry and environmentalists backing job-gaining industries and the beauty of Tasmania.
"The leaders of the government and the opposition ... I'm very happy to take them out there."
A third activist, Syed Ali Imran Alishah, has pleaded guilty to one court of trespassing relating to the February 19 protest.
He also pleaded guilty to trespassing after illegally remaining on land in the Styx Valley three days earlier and was listed to face a disputed facts hearing on Monday.
Alishah has been in custody since being arrested at the protest and conducted a hunger strike in prison.
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