There seems to be something wrong with our bloody ships today," remarked a British admiral at the Battle of Jutland, as he witnessed his fleet being depleted one after another by enemy fire. Pharmaceutical regulators in Europe today might be forgiven for entertaining a similar thought about their institutions.

The latest and most dramatic blow—the abrupt departure of health commissioner John Dalli in highly controversial circumstances—comes on top of an extremely difficult year for the European Medicines Agency. The European Commission and the EMA are two principal arbiters of control on medicines in Europe—the twin pinnacles of the European Union's regulatory system. And they have both been severely shaken.

At the same time, one of the main supervisory bodies for all the European Union's institutions—the European Court of Auditors—has admitted to a crippling weakness: It announced this month that it ran a check last year on what was going on at the EMA, and found disturbing evidence of mismanagement, but it doesn't have a clue about what has happened since 2011.

The Dalli débacle is disconcerting in many ways. The European Commission's mid-October announcement that he had stepped down from his post "with immediate effect" in the wake of an anti-fraud investigation sent shockwaves through Europe. The link that the commission made to suggestions of corruption in decision-making compounded the concern.

But on closer inspection, the announcement did more to provoke questions than to supply answers. It did not accuse Dalli of any evident misdemeanor, but merely alleged that he was aware of attempts by others to traffic influence (in relation to legislation to control tobacco rather than medicines). On top of that, it recognized that in any case no transaction was concluded and no payment was made. It did not say Dalli had been fired, but merely that he had "decided to resign in order to be able to defend his reputation and that of the commission."

Dalli, summarily stripped of office, immediately riposted through his own channels. He rejected any suggestions of guilt, and claimed that he had been forced to resign by commission president Jose Manuel Barroso. Worse, he went on, Barroso had presented no evidence of wrongdoing, but had merely shown him the summary of an investigation that had been secretly underway for five months.

The bizarre sequence of events inevitably prompted further speculation. If Dalli had merely been aware of a lobbying attempt by a vested interest (and the commission made no accusation beyond this), why should he be obliged to resign, it was asked. Lobbying of commissioners is an everyday routine in Brussels, and is considered a normal and indeed necessary part of the discussions that underpin the preparation of any legislation. Logically, every commissioner should be removed from office if they were to be treated in the same way as Dalli. So had Dalli transgressed in some way that the commission did not reveal? Or, if he had not, was there some other reason that determined Barroso to get rid of him? Or had the commission over-reacted and fallen into a trap set by business interests? Dalli's departure will delay progress on new tobacco-control legislation that is vigorously opposed by the tobacco industry.

The commission has done nothing to answer these questions, or to clarify the extraordinary procedure, and a cloud of suspicion consequently hangs not only over Dalli, but over the commission itself—and not just in relation to possible impropriety, but also over what looks dangerously like incompetence and mismanagement.