In December 2010 Thomas Lonngren stepped down as the executive director of the European Medicines Agency, which regulates the pharmaceutical industry. On the 28th of that month, he sent a letter telling the management board that he was going to start working as a private consultant to the industry on 1 January.

Some places have clear regulations on this kind of thing. In the US you have to wait a year after leaving the department of defence before you can work for a defence contractor.

But after 10 days, Pat Mahony, the EMA's chairman, wrote back saying the plans were fine. He did not impose any restrictions, nor did he ask for any further information on what kind of work Lonngren intended to do. Lonngren had said there would be no conflict of interest, and that was enough.

Why does this matter? It's an old story, after all, and the flow goes both ways. One of the pharmaceutical industry's favourite lawyers has just become head of the US Patent Office. Employees at the the US food and drug administration (FDA) routinely flow in and out of pharmaceutical companies. The UK lobbying industry is built on the same phenomenon.

There is no a guarantee of a bad outcome here: it's just a risk factor, like driving after three pints, and so we police it. Perhaps civil servants will be too friendly to industry, hoping for a lucrative commercial post one day. At the very least they bring insider knowledge of opaque systems, and personal contacts, which are the cornerstone of effective lobbying.

In a fully transparent regulator, we could perhaps tolerate these risks. But sadly, it's not just the natural opacity of a technical field that forces us into a blinder faith on regulators.

When the FDA discussed banning rosiglitazone, as I described six months ago, for all its bad calls, these discussions were at least in public. For the EMA, all such meetings and minutes are secret.

The key ethical issue in medicine is that the results of trials are left unpublished by industry (and others) if they don't like them. We have seen this with rosiglitazone, paroxetine, countless antidepressants, and many more drugs. The solution was to start clinical trials databases: you declare what you are doing, before you start, and we can hold you to it, and ask about missing data when the results don't appear.

The EMA's clinical trials database, Eudract, has run since 2004, and has been held entirely in secret despite repeated promises to open it up going back many years (they're promising this month, again).

I can tell you that this database contains 28,150 clinical trials, but that is all we are allowed to know. We cannot read a single detail about any single one of these trials, which are all of real treatments being tested on real people. This is bizarre and far more important than the story of one man's employment. It is the ultimate administrative perversity: Eudract is a transparency tool held in secret.

To regulate the pharmaceutical industry behind closed doors is the antithesis of science. But the EMA have made their decisions about this, so we are left with blind faith, at an inevitable cost.

Everyone involved in such a system must be seen to be whiter than white, not because we are puritans, or assume bad faith, but because, after the secrecy, this is what they have left us with.