In an interview with The Associated Press, the 78-year-old producer and ambient music pioneer put most blame on those who blocked the shows.
"The people we should really be pointing at are the people who didn't permit the show to go on," Eno said.
"I mean, Ed, I think, was weak. He could have said 'I'm an artist. You hired me as an artist. That means you get my decisions about what the band should be and who I'm playing with.' He could have insisted on that."
The dispute began with Macklemore's sets at MetLife Stadium in New Jersey on September 4 and 5. During the performances, he displayed images from Gaza and urged the crowd to say "Free Palestine."Â
The US rapper rejected claims that speaking against Israel meant he hated Jewish people.
Sheeran gave his account in a public statement, saying Macklemore's contract was with the promoter.
"Macklemore coming off tour was the promoter's decision, it was not mine," he wrote on social media.
Eno also told AP that he had reservations about artificial intelligence, particularly the concentration of power in the hands of a few tech giants.
"I'm fascinated by the possibility of working with it. My problem with AI is the ownership of it and what I know are the moral and social values of the people who own it. And they are really some of the worst people to be in charge of something as powerful as that.
"And of course, the other problem is because they're all so chasing the dollar so earnestly, they're in competition with each other, so they're trying to outdo each other only in terms of winning that particular competition, not in terms of what benefits the world."
The former Roxy Music star said regulation of AI was crucial.
"The evolution of a technology, that means the time when it is emerging, is very important.
"And it's very important that the public is somehow engaged in that. Otherwise, you end with this ludicrous situation we have now, of agentic AIs that are far too powerful for any of us to understand at the moment, including the people who make them. It's a real failure of regulation."