The outspoken TV star, 56, shared a clip of the climate activists at the Port of Dover.
"Just drive over them," he quipped on Twitter.
"Fewer people is good for the planet anyway. Win-win."
However, his words angered some people, with some claiming his joke was "offensive" and "irresponsible".
"Shameful thing to say," said one person. "You may not like what they are doing but there is a very real issue that they are bringing to the fore."
"This would be a fairly irresponsible tweet if you were using a social media platform where you had, I don't know, say 8 million or so followers," said another.
"Interesting comment from a champion of free expression, and self-appointed bastion of rationality and moderation, such as yourself," said another.
However, others pointed out that Morgan's comment was clearly a joke.
"It's just a joke, remember those???" said one.
Another person tweeted: "Whilst I get your point and frustrations Piers you cannot say that sort of thing in these new times. It gets you cancelled. Have we come to a stage now that nothing can be said even in jest or your (sic) cancelled. I think we have indeed."
Insulate Britain has blocked parts of the M25 motorway several times recently.
The group wants to raise awareness of the climate crisis and wants to see UK homes insulated to help cut emissions.