Farmers have been protected from the real world of legislation too long said the head of the Scottish Environment Protection Agency (SEPA) this week.

Dr Campbell Gemmell, chief executive for the past three years of a quango that is a regular target for criticism by NFU Scotland, said that no industry liked legislation such as the water framework directive, waste disposal, pollution control and water abstraction licensing now being applied to farming. And some, including Scotland's paper-makers, had finances every bit as precarious as farming, he said, the usual reason given by the NFU for objecting to legislation.

But, he told a press briefing at SEPA headquarters in Stirling, other industries, such as chemical manufacturers, have lived with legislation for much longer and have a distinctive and influential representative organisation prepared to discuss and help influence its direction.

He went on, possibly to the consternation of the NFU: "With agriculture it is obvious that it's a long way from that model. Engagement with the sector has not always been good and still isn't." Part of the problem, he said, was that agriculture had been protected from much legislation by its special relationship with government, and now the Scottish Executive, a relationship no other industry had. That was why farmers, or at least the NFU, thought the industry was now faced with massive challenges, "and it sticks in their craw." He was particularly critical of the furore about water abstraction rates and licence fees. There had been two years of talks with the NFU, said Gemmell, when the union could have made suggestions. They did not, then complained bitterly when SEPA announced its proposals and even more about proposed charges, although he agreed these have been modified. He said that the union struggled to represent its members and did not necessarily represent all farmers: "It would be good if NFU Scotland was in a position to speak for the whole farming sector and that has not always been the case."

Claiming that many farmers, possibly the more progressive, agreed with SEPA's efforts to improve the environment and water quality by implementing legislation it was duty-bound to enforce, Gemmell suggested that farmers should come in to the real world. Complaint about legislation as a first reaction was "a council of despair", he said.

SEPA, set up ten years ago, was not gold-plating European Union rules and in many cases, the legislation should have been enforced much earlier: "We have a burden of environmental legislation to implement and it has grown dramatically. But some of it the UK signed up for in the 1970s, 1980s and 1990s. If it had been introduced when it should have been we could all have had a shallower learning slope."

That had been recognised by the Executive and environment minister Ross Finnie, he said. But there was no point in farmers complaining, for example about water abstraction rules: "If you are taking 100,000 litres of water a day for irrigation, that's enough for 6,000 people and a serious business... Water is a scarce resource and it's an outmoded notion that water running round your farm should be free."

He accepted that SEPA had made mistakes, not least in communications. But he insisted that it was up to farmers to adjust their thinking on water use, waste disposal - "we found at recent road shows that some people on this planet still think that burning plastic is a good idea" - and pollution prevention. "We all have a vested interest in a thriving Scotland. Do we always want to be at the coo's tail? Is it a good message to put out 'Come to Scotland, we cut corners'?"