When Hughes accepted the role as the first chief executive of the new regulatory body he was handed 23 investigations - only a handful of which had actually been started. Three years later and there are just three cases still under the magnifying glass - St Laurence Finance, Mutual Finance and Viaduct Capital - and Hughes expects decisions soon on their outcomes.
He faced a mammoth task with investors feeling burned by failed finance companies and let down by the Securities Commission.
"Sitting in Australia thinking about the job and thinking about what I would do first - the only things I heard were criticism of the Securities Commission and the collapse of the finance company sector. It wasn't a palatable picture. I knew the initial establishment phase was going to be a tough ask; changing people's roles and perceptions both from a regulator and regulated."
The organisation has won respect from the industry for its engagement and it has been quick to take action against those who have broken the rules.
Hughes counts his biggest achievement as positioning the organisation to gain that market perception. It has also managed to attract top talent which he puts down to building a base in Auckland.
He says moving into Auckland has given the FMA "real-time visibility".
"People see us as part of the market."
But he is frustrated that there is still an element of misunderstanding at times and what he calls blatant ignorance. "We are not here to act as a capital guarantee on investments. Nor are we here to pursue every lawbreaker".
The FMA has faced some criticism over the collapse of Ross Asset Management.
Wellington-based financial adviser David Ross was licensed by the FMA under a regulatory regime it helped to introduce. But that didn't stop him running a Ponzi scheme which lost millions of dollars of investors' money.
"It's a fact that the FMA authorised David Ross. Based on the information we had we didn't have any mandate to perform additional merit-based checks that some have suggested we should have done.
"There was no information suggesting Mr Ross was not a fit person."
Some have also questioned how quickly the FMA acted.
But Hughes said that within a matter of days it had frozen his funds, appointed receivers and had him in court.
"You won't find a regulator that has acted faster. We seem to be criticised for not stopping him. I will wear it on the chin. But if others say they knew all about it and didn't report it - who really is the guilty party?"
The FMA is about to expand its regulation of the industry with auditors and trustees already in the process of licensing and fund managers still to come under new securities law the Financial Markets Conduct Act.
It will oversee around 30,000 people when it all comes into force next year. That will be a challenge with just 150 staff.
"It's inevitable with that many people the FMA can't be everywhere."
Hughes says that means the organisation has to become more and more reliant on risk-based strategies and intelligence gathering.
"We need to get smarter in the way we use intelligence. It also means they will have to judge the information they get from licensing to place the applicant on the risk spectrum.
"If we don't do that we will only ever be behind the eight ball."
Hughes says it isn't counting on any more money to fund the organisation. But it could mean the way some levies are charged will need to be recalculated so that those who pose the highest risks are charged more.
"If you are a higher risk you are going to require more attention from the FMA."
But he also says no regulations are ever going to be totally foolproof.
Hughes says investors should not be afraid of the market.
"If you want to make money you have to take some risks. The best thing is to arm yourself with information. Don't slavishly follow advice or methods others have adopted.
"Talk to friends, family members, financial advisers, read the newspaper. Pause before you invest. Don't be led by a high rate of return. Above all, ask if you are prepared to lose the money. If you can't afford to lose it, don't invest."
Hughes says for the majority of Kiwis, KiwiSaver should be their main investment outside of their home.
"It will be professionally managed. The portfolio will be spread across a variety of investments and hopefully the fees will be affordable. If you are lucky enough to have money over and above that take precautions and shop around."
His major regret is not doing more to aid financial education but he says the sector needs a conductor to lead the orchestra of the main players involved in that area.
"I think all of us in the public sector are looking for a clear steer. We've all got different instruments to play."
Hughes does not have a job to go to. He's had a few nibbles but says the only thing he really wants to do right now is have a break.
"It's not a role where you finish on Friday and come back on Monday. You reach a point where you say I don't have anything more to give."
He's heading back to Australia to join his family for a two-week cruise around the South Pacific.
Sean Hughes
Age: 47
Born: Palmerston North
Education: Bachelor of Laws and Bachelor of Arts from the University of Canterbury, Master of Law from Cambridge University in the UK.
Family: Married, two children.
