Ward will step down from the chairmanship in the spring after what must seem like a five-year marathon, much of it dominated by squabbles and a little sensible debate over its structure. The agency is now raring to go, but a lengthy and generally inward-looking focus by a highly paid management team and its political masters has done nothing to curry favour with its critics, who still wonder whether it is worth the money that taxpayers pour into it.

Ward believes none of this should detract from the agency's role and importance to the economy and its contribution to Scotland's future status or performance. So what does he say to those who maintain that it is past its sell-by date, no longer contributing anything that others couldn't do, and should be wound up?

"My goodness, you don't want to do that," he says, indignantly. "You would scrap the bioquarter (in Edinburgh], the co-investment fund, the translational medicine project (a collaboration between SE, four Scottish universities, the NHS and US pharmaceuticals firm Wyeth]. These are hugely valuable to Scotland. This organisation is uniquely placed to do these things."

At 68, and with a string of senior positions on his CV, Ward is preparing to wind down himself, but until he retires he'll remain fired up by the arguments over SE and why it deserves protection and support.

He was working abroad in the Seventies when he first became aware of how Scotland was underplaying its assets. While director of IBM in Scotland he set up the Scottish Electronics Forum to help raise the level of value-added activity and, since 2004, when he moved into Atlantic Quay alongside chief executive Jack Perry, he's been focused on much the same agenda.

"It remains our key problem. How do we get our assets into the marketplace? We have high employment, high skill levels, but low productivity. It is because we are not putting enough value through the system."

At least some things are changing, including the political culture, which he regards as much more in tune with business thinking. "I thought that getting the value-added message across would be a hard sell. I now find it generally accepted that we have to create value. The body politic has moved a long way and now doors are open," he says.

Ward likes the textbook approach to getting results and peppers the conversation with references to pyramids, bubbles and silos. It all sounds so logical and indisputable, but the process-driven agenda may also appear unbending and formulaic. This economic development by numbers doesn't seem to leave much room for the touchy-feely aspects of helping businesses to grow. Critics say some of the advisers don't understand their problems; others claim they never see the same adviser twice.

"When we have done surveys we found that those we have dealt with give us a high rating. Non-customers give us a lower rating. Yes, we do have to touch more people," he concedes.

SE has at least been able to take the business lobby groups with it, and they remain largely supportive of what it is trying to achieve. CBI Scotland director Iain McMillan sympathises with Ward and Perry over the time it took to instigate the reforms they wanted when they first came on board. "The changes that John and Jack wanted several years ago got snarled up in the last Scottish Executive, which was frustrating for them and also for those in the business community who supported the changes," he says. "When the new Government took over, John Swinney (the Finance Minister] wasted no time and by and large put in place what SE had been calling for."

McMillan, however, shares some wider concerns that the Business Gateway programme for small firms was switched to local authority control, a view that some senior figures at SE would privately share. But slimming down SE to its core functions of supporting business growth and developing key industries has been broadly endorsed across the political and business spectrum.

Ward believes that relieving SE of developing individuals has been the right decision, and Careers Scotland was the biggest of the functions moved out of the organisation. It has left SE a fraction of its size. Careers Scotland took 1,200 staff and another 260 accepted voluntary redundancy, leaving SE with 1,050 on the payroll.

The number of programmes has been slashed from 700 to 70 and the budget will fall to £283m, half its recent level. Its annual report showed it hitting all its targets.

But controversy continues to surround those big salaries and pensions for its senior staff. Chief operating officer Lena Wilson famously earns more than the Chancellor of the Exchequer and the Foreign Secretary, while Charlie Woods, another former director, saw his pension pot rise to £720,000 on his early retirement. Such payments help confirm in the minds of critics that SE is merely a gravy train for civil servants.

The row over the budget overspend a couple of years ago gave opponents more ammunition to fire at the agency, though insiders who were unable to speak out at the time said it was a lot of fuss over a balance sheet issue that got overstated. "The reality is that in terms of cash flow in the organisation it didn't make any difference," says Ward dispassionately. "Jack got a tough time over it and we all got a fair amount of criticism, but I'm not sure those who were doing the criticising actually understood what was driving it."

Ward believes critics have to see the bigger picture and understand that Scotland is no different to other countries in requiring a development agency to help lead and nurture its economy. He is defensive about the ITI research bodies, despite their ability to shed senior staff at a rapid rate.

Senior insiders admit that the £450m 10-year programme is under review, and Ward is diplomatic about their performance and future. "They are more or less where they said they would be," he says, without commenting on further criticism that they are almost halfway through their lifespan without having produced a single company.

Ward and Perry will admit some programmes have slipped, but both also share the desire to create an agency that is not afraid of risk. If that means there are losers as well as winners, so be it. "Some of the fundamental problems are still there and are cultural," says Ward. "But if Scotland makes the most of the assets it has then it is going to win."