Thunberg and dozens of other environmental campaigners on Monday began blocking the main entrances to Sweden's parliament in a sit-down protest against the effects of climate change and what they said was political inaction.
Police did not intervene at first, but removed the demonstrators when the protest resumed on Tuesday morning.
Thunberg, 21, became the face of young climate activists as her weekly protests, starting in 2018, in front of the Swedish parliament quickly grew into a global youth movement with large rallies across continents.
Stockholm police have said that although activists had the right to demonstrate outside the national assembly, they were removed for blocking entrances.