"I thought he would move with 300 to go and he didn't move he went backwards. I was just shocked because he's promised us a lot... I was hoping he would get this one today because I thought this was his opportunity. His chance.
"I don't want to condemn the boy. But I was disappointed because I expected more."
A training issue or a problem with his recovery could have limited Willis in the final, Sir John said.
"At the end of the day only he knows what went wrong. He's the one that's going to suffer most."
Sir John said Willis should now wipe the slate clean and focus on the rest of his career.
Willis this afternoon took to Twitter to explain what may have been behind his performance in the race.
"On reflection my poor performance wasn't likely a miss-timed peak, but inability to recover from rounds. How to fix that is the Q," he said.
He was thankful for the "overwhelming" support he had received.
"This Olympics has still been an amazing unique chapter in life."