The 54-year-old Dutchman is quitting after the failure to reach his own target of eight British Olympic medals in track and field.
UK Athletics yesterday announced that their current head of sports science, Neil Black, will be the new performance director whose first job will be to appoint van Commenee's successor.
Van Commenee was adamant he could not have stayed on after failing to reach the target – a total of six athletics medals was two short – and when asked if he had any regrets, suggested he had not been tough enough.
"I think I compromised too much," he said. "I am the soft factor here. I am the mellow one. I compromised too much and for that reason we could have done better.
"I put some pressure on but I think we lost some medals because of coaching. We should have compromised less in that area [and] certain behaviours from individual athletes."
Van Commenee would not cite individual cases but he had a well-known fall-out with Phillips Idowu over the triple jumper's use of Twitter, and the athlete, one of Britain's top medal prospects, went missing just before the Olympics with an injury.
Van Commenee said he still felt proud of what had been achieved, but the time had come to move on. "I don't get emotional very quickly, but on Super Saturday [when three golds were won] I was very affected," he added.
"But I am most proud of the culture that we have set together, a high-performance culture that has enabled us to develop. I meant that we got rid of the cynicism and negativism around our sport. That makes me really proud.
"One of the pillars under that culture is accountability and accountability comes with targets.
"Targets are a serious issue. I was trying to imagine how it would look for me and the programme were I to stay. For me, these conversations would have been incredibly difficult because every time I would talk about it, it would be: what does it actually mean, what are the consequences? I am gutted that we didn't hit eight medals. So I have no choice. For the programme it's the best thing that someone else takes over."
Van Commenee voiced his approval for Black's appointment, saying he would be "my first recruit" in any athletics organisation.
Niels de Vos, the UK Athletics chief executive, described van Commenee as the "rocket fuel" that had been needed to spark life back into a sport that was in the doldrums but that this could be the time for new blood.
He said: "I talked about Charles being rocket fuel, but rocket fuel burns people as well as propelling the organisation forward and sometimes the person who started the process may not be the best person to do phase two."
Black comes with his own reputation for toughness – former heptathlete Kelly Sotherton described him as "harder than a conker soaked in vinegar" – and he confirmed Canadian Kevin Tyler, who has been UK Athletics' strategic head of coaching and development since 2008, will be a "strong contender" to take over from van Commenee though there are a number of candidates including at least one woman.
He is the first performance director for the organisation since Dave Collins left in 2008.
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