When it comes to the thorny issue of scientific misconduct and how to police it, Germany is a role model for many. Its main research-funding agency, the DFG, published exemplary guidelines in 1998 to steer good scientific practice in universities.

The guidelines comprise 16 recommendations, and are effectively mandatory because universities that do not sign up to them are not eligible to receive DFG grants. Among the recommendations are mechanisms to drum the importance of honesty into trainee scientists, and a requirement for each university to appoint an independent mediator to whom young scientists can turn in confidence in cases where they suspect misconduct. The DFG also created a central ombudsman system to handle disputes that cannot be resolved locally.

The DFG formed the recommendations after a landmark 1997 fraud case in Germany that shook the academic community to its roots. A pair of clinical researchers had been systematically fabricating research results for almost a decade; in the final count, more than 100 papers were implicated.

It was the digital revolution that allowed their faking to remain undetected for so long — they could cut and paste gel images and other data on their computers at a time when referees were not tuned into such tricks. And in Germany’s rigidly hierarchical academic system, they were able to control any potential leaks from their labs. As star professors who had soared through the academic ranks on the back of their publication lists, they were easily able to intimidate any research student daring to query how papers were generated overnight when experiments seemed not to have been done. Any whistle-blower would lose all career prospects.

The digital revolution has continued, and so have the scandals. Plagiarism is the latest trend, and recent years have seen leading politicians exposed for cheating in their PhD theses. Remember Karl-Theodor zu Guttenberg? The aristocrat soared through the political ranks to become Germany’s defence minister in 2009. But in early 2011, plagiarism hunters found that parts of his thesis had been copied, told the press and forced his rapid resignation. After zu Guttenberg came a series of similar exposures involving high-ranking politicians in Germany, where a PhD is an advantage in politics. The revelations devastated careers.

The DFG has put the universities in a difficult position.

Anyone with a computer can now run plagiarism software. Some have wielded it for great good, such as the website Integru.org, which has exposed deep academic and political corruption in Romania. But in some cases, the software seems to have been used for smearing, or at least for the thrill of the chase. Many, for example, were unconvinced by accusations of plagiarism against Germany’s education and research minister, Annette Schavan. But enough publicly thrown mud managed to stick, and she was forced to resign in February.

With the rise in digital scrutiny and increasing legions of self-styled fraud-busting bloggers, the DFG is rightly concerned about the need for due process. Is it right, for example, that the accused is named while their accuser hides behind Internet anonymity?

Last week, the DFG updated its scientific-practice guidelines to underline the benefits of its system, which, as far as possible, facilitates a confidential, fair and thorough investigation of charges. Its latest recommendations now emphasize the value of a whistle-blower, and the importance of protecting him or her at all costs. It warns against breaking the confidentiality of an ongoing investigation by going public with names. It explicitly notes that all accusations must be made ‘in good faith’, stating that ‘bad-faith’ accusations may also be considered a form of scientific misconduct, and that anonymous complaints may not be followed up.

All well and good — but this time the DFG has formulated its recommendations surprisingly poorly. The consequences of breaking confidentiality, or of being charged with accusing in bad faith, are left open, prompting conspiracy theorists to fill the blogosphere with wild charges that the DFG is gagging the scientific community.

That is far-fetched. But it is true that the threat of punishment for accusations that cannot be proved could make even the most confident whistle-blower nervous to move forward. And in announcing its updates, the DFG has not addressed a key issue that makes whistle-blowers go public in the first place — the justified fear that the procedure will drag out, while no one knows what is going on.

The DFG has put the universities in a difficult position. It is universities that investigate claims of misconduct against their own, and therefore the universities who will be asked to implicitly convict whistle-blowers if their information cannot be confirmed. The DFG should take care to explain how and when sanctions would be used, and what those sanctions are likely to be.