Toni Minichiello, who has coached the heptathlete since she was 11, claimed an unnamed "high-ranking person" told him: "She's fat and she's got too much weight."
Ennis, who won a silver medal at last year's World Championships, is considered one of Britain's leading medal hopes.
The 26-year-old's attractive looks have made her a poster girl for London 2012, and was chosen to model the Stella McCartney-designed British Olympic kit.
Minichiello dismissed the criticism, saying it was typical of distractions to Ennis's preparations that he was trying to filter out.
"I get emails, phone calls, text messages and voicemails giving me advice on what I should be doing with Jessica Ennis that's going to make a difference," he told The Guardian. "It's a lot of background noise that you can get easily distracted by.
"I always read it and have a look and think maybe there is something there. Yes, it might be a great idea, but it's not a great idea for today, it's a great idea for next year. I've never had any issue with her weight or shape. There are times I've wished she was taller, but that's it."
Minichiello conceded Ennis's celebrity status represented another distraction.
"The difference is that she's now a 'personality'," he said. "If she walks into the dining room, people will go 'Ooh, that's Jessica Ennis from athletics.'
"Equally, she'd turn round and go 'Wow, that's David Beckham on the Great Britain football team.' So there's lots of distractions."
UK Athletics declined to speak to the Guardian on Thursday night.