On the face of it, the Scottish Environment Protection Agency (Sepa) has done something right. It has taken action aimed at reducing the toxic pesticides dumped in sea lochs by salmon farms.

A scientific study has found evidence that one pesticide, emamectin, is killing more seabed wildlife that previously thought. Science has suggested a problem, and the Scottish Government’s watchdog has responded.

But unfortunately that’s not the whole story. Sepa’s move came a few days after our front page investigation last weekend revealing that 45 lochs were contaminated in breach of environmental safety limits. It also immediately followed the release of internal emails under freedom of information law to an anti-fish-farming campaigner.

Those emails show that Sepa was originally planning to highlight a scientific study regarding fish farm pollution. But the way it was planning to do this was not in line with the agenda of the fish farming industry, which asked Sepa to hold fire.

Sepa complied, and ditched an article it was planning to publish. We don’t know for sure what Sepa was planning to say then, but presumably it would have borne some resemblance to what it said last week.

So it looks like Sepa delayed expressing concern about pollution because the fish farming industry was unhappy, but then eventually acted after public attention was drawn to the issue by this paper. Is this how a regulator should behave?

We have expressed concern before that Sepa is getting too close to the businesses it is meant to be regulating. There is now substantial evidence that this is the case with the £1.8 billion multinational fish farming industry.

But is the same true of Sepa’s relationship with other industries? There have been criticisms of its links with the whisky industry, and worries about “light touch” regulation. Sepa now needs to explain itself, and Scottish ministers should take a closer interest in how it is actually operating.

It would be short-sighted - and very sad - if the agency that was meant to be protecting the environment for future generations turned out to be compromising it for the benefit of business.