"Four arrests have so far been made at the obstruction incidents at Stratford and Canning Town on the Jubilee Line," British Transport Police said in a statement.
A similar protest hit east London's Shadwell station, on the Docklands Light Railway, which interrupted morning rush hour service into the city centre, an AFP reporter said.
Police gave no more details, but video posted on social media showed several men climbing on top of trains at Canning Town on the Jubilee Line, which links northwest and east London via the city centre.
Furious passengers dragged at least one protester from the train as station staff tried to intervene to prevent violence by irate commuters.
Environmental pressure group Extinction Rebellion confirmed its members had conducted "non-violent disruption" at two stations and that there was an "incident of violence" against a protester at Canning Town.
It said later that two of the protesters who climbed on top of a train at Shadwell station were priests -- one Catholic, the other Anglican.
A third person, said to be an 83-year-old former parole officer, glued himself to the side of the train before saying prayers with other members of the group.
BTP assistant chief constable Sean O'Callaghan had urged protesters not to target the Tube or rail network, which he called "one of the greenest transport methods" in London.
London's Metropolitan Police has arrested more than 1,600 protesters since the group's "Autumn Uprising" began on October 7.
Extinction Rebellion, which wants the British government and others around the world to do more to cut carbon emissions, is challenging restrictions on demonstrations in court.
The group said it would be highlighting the effect on the climate of air travel by handing out leaflets at London Gatwick airport on Thursday.
But it added: "There is no intention to disrupt flights."