William Sitwell made the comments after a vegan journalist wrote to him pitching an idea about a plant-based meal series.
In response, Sitwell wrote: "Thanks for this. How about a series on killing vegans, one by one. Ways to trap them? How to interrogate them properly? Expose their hypocrisy? Force-feed them meat? Make them eat steak and drink red wine?"
Buzzfeed published his response to food journalist Selene Nelson, and contacted Sitwell, who said he was sorry 'to anyone who has been offended or upset by this'.
"I've never seen anything like it," Nelson told Buzzfeed. "I've written about many divisive topics, like capital punishment and murder cases and domestic violence, and I've never had a response like that to any of my articles or pitches.
"And he's the editor. He's representing Waitrose and he's talking about 'killing vegans, one by one'?...I'm not judging people who eat meat - I wasn't a vegan for 28 years of my life. But having such an angry, vitriolic response to someone who's simply trying to reduce the harm they cause to animals and the environment is something I can't understand."
Apology to vegans
Initially, Sitwell apologized, saying: "I love and respect people of all appetites be they vegan, vegetarian or meat eaters, which I show week in week out through my writing, editing and broadcasting.
"I apologize profusely to anyone who has been offended or upset by this."
A spokesperson for Waitrose added: "Even though this was a private email William's gone too far and his words are extremely inappropriate, insensitive and absolutely do not represent our views."
But now it has emerged that Sitwell has resigned. A spokesperson for Waitrose said he will be leaving with immediate effect. "We have been informed by John Brown Media, who produce the Waitrose & Partners Food Magazine, that William Sitwell is stepping down as Editor of Waitrose & Partners Food magazine with immediate effect," said a statement.
"In the light of William's recent email remarks, we've told John Brown Media that we believe this is the right and proper move - we will be working with them to appoint a new editor for the magazine.
"We have had a relationship with William for almost 20 years and are grateful for his contribution to our business over that time."