De Jong's role as HPD was to manage the programmes of the international teams. He employed the staff for each team and would then manage the campaigns and oversee the administration.
"The roles and responsibilities of what happened with the Olympic campaign will come out later in the piece, but right now I'm comfortable with the accountability," said de Jong.
NZF are still hoping to overturn their disqualification in an ongoing legal battle with OFC, but de Jong said that regardless of the outcome it was time to step down.
"With my time in the role there are things I look back on with a great deal of satisfaction and there are some things I look back and go, 'could I have done better', or, 'Should I have made a different decision?' But at the time you make a call based on what you think is in the best interests of New Zealand Football.
"Because we are in the middle of a legal process, I'm not going to go into the ins and outs of the eligibility side of things, but I will say I accept a level of responsibility for what has happened."
The cost of the administrative error from NZF is expected to be measured in millions. If they had won their final, the Oly Whites were guaranteed five top-class matches, with at least three at the Olympics as well as warm-up games. Under that scenario, almost all costs were covered. An equivalent series of matches would cost up to $1.5 million to arrange.
NZF have also shelled out thousands of dollars on legal expenses along with qualification camp costs estimated at $100,000.
Asked if he feels he has left NZF in a better position than when he took over, de Jong said: "I'd like to think so. We didn't have a high-performance director when I walked in the door and some of the structures we have put in place are an improvement on when I arrived."
De Jong highlighted his role in the planning and early delivery of NZF's elite game blueprint, the Beyond Football plan, and the activity he helped give to New Zealand's age-group and senior teams with limited resources.
"The biggest challenge (in the role of HPD) is managing expectation alongside the resource that football has in New Zealand, across all our international teams. That will always be one of the trials for a high-performance director."
De Jong plans to take a break with his family but will not be a stranger from television screens due to his commentary role with the Wellington Phoenix.
"That's up to Sky. They typically ring me up and see what's available, so we'll see how that goes."