The star prompted a backlash after flying 5,400 miles to attend the climate change protests in Oxford Circus.
But the actor said she has reduced the amount she flies, before referencing the suffragettes while discussing the disruption the protests have caused.
Activists have been protesting since Monday, occupying the main intersection of Oxford Street and Regent Street and setting up a camp at Marble Arch.
Dame Thompson said: “Unfortunately, sometimes I have to fly, but I don’t fly nearly as much as I did because of my carbon footprint and I plant a lot of trees.
When asked if she flew economy, Dame Thompson said: “I b****y don’t, no, I’m far too old for that.”
“One of the things which has happened consistently over the decades I’ve been protesting about this is that it’s always turned back on the individual – you’re the one who flies, you’re the one who’s using this, you’re the one who wants this.
“The fact of the matter is, everyone has been asking for clean energy for decades – this demand has been made for decades and it has been ignored for decades.
“If I could fly cleanly, I would.”
She added: “I’m sure everyone feels the same, that to inconvenience people and disrupt their lives is not desirable, but sometimes, as the suffragettes would have said when they were fighting for the vote and let us not forget they disrupted an awful lot of people’s lives in order to get something which we now take for granted.”
Asked about wasting police resources, the Sense and Sensibility star said: “That’s up to the police, that’s not our decision, we didn’t ask for police resources.
“It’s not like we’re burning things down. The police turned up because they’ve been asked to turn up and that’s not our responsibility.
“You ask the government about that or you ask Westminster about that, they decided to spend their money in this way, which I think is a waste of taxpayers’ money – we’re not doing anything violent.”
There have been more than 570 arrests this week across London linked to the protests.
Ten people had been charged by the force by Thursday night and three others arrested by British Transport Police were remanded in custody after they appeared in court accused of obstructing trains at Canary Wharf.
Shortly after Dame Emma's address, a team of police officers encircled the boat and told bystanders there was an ordinance to clear the area.
Police pushed bystanders further away from the blockade while dozens more officers moved in.