She is due to appear in court in the southern Swedish city at 0930 GMT.
The 20-year-old activist “participated in a demonstration that obstructed traffic” and “refused to comply with police instructions to leave the site”, according to the indictment seen by AFP.
She faces a maximum sentence of six months in prison, but such charges usually carry a fine, prosecutor Charlotte Ottosen told AFP.
The rally, organized by the environmental activist group “Tatilbaka fårðin” (Reclaim the Future), attempted to block entry and exit to the port of Malmö to protest the use of fossil fuels.
“We are choosing not to be bystanders, but instead to physically stop fossil fuel infrastructure. We are reclaiming the future,” Thunberg said in an Instagram post at the time.
Thunberg rose to global fame after launching a “school strike for the climate” in front of the Swedish parliament in Stockholm at the age of 15.
She and a small band of young people founded the Fridays for Future movement, which quickly became a global phenomenon.
In addition to her climate strikes, the young activist regularly slams governments and politicians for not properly addressing Weather problems.
According to a preliminary transcript seen by AFP, Thunberg responded with “no comment” to police questions about the Malmö rally.
Despite legal pressure, Reclaim the Future remains unwavering in its determination to stand up to the fossil fuel industry.
“If the court decides to treat our action as a crime, it may do so, but we know we have a right to life and the fossil fuel industry stands in the way of that,” group spokeswoman Irma Kjellström told AFP.
Six members of the organization will appear in court in Malmö, she said.
“We young people are not going to wait, but we will do what we can to stop this industry that is burning our lives,” she said, explaining the group’s plans to continue breaking the law.