Over the next couple of months, every government department will be explaining to the civil service commissioners exactly how they deal with alleged breaches of the civil service code. The work has been requested by first civil service commissioner Janet Paraskeva; she is worried that very few civil servants, unwilling to use their own departments’ complaints procedures or dissatisfied with their outcome, have complained to her about breaches of the code.

The scarcity of eligible complaints to the commissioners – totalling just six in 2007-08, two in 2006-07, and none from 2003 to ‘06 – might strike less scrupulous observers as a sign that all is well with departments’ own systems for handling allegations of breaches.

But last year 27 allegations never made it beyond departments’ internal complaint handling systems; Paraskeva is at pains to ensure that the low numbers reaching the commissioners don’t reflect either a fear of making allegations among civil servants, or a tendency for departments to smother complaints.

Earlier surveys on this topic by the commission received patchy responses, and Paraskeva says this external audit will be “much more rigorous”. Cabinet secretary Sir Gus O’Donnell is an enthusiast, and gave Paraskeva the opportunity to collar permanent secretaries at one of their recent weekly meetings; she is determined to involve senior managers, including HR directors, complaints handling officers, heads of internal audit and permanent secretaries.

The results, due to be published in July, will reveal little to the public: Paraskeva has ruled out “naming and shaming” departments, preferring to offer good practice examples that could “set a blue print for others”. Instead, any specific concerns will be raised with permanent secretaries and the Cabinet Office.

FDA general secretary Jonathan Baume doubts that the trawl will reveal any serious problems; he believes that senior managers have a good grasp of the code, and that the low numbers of complaints are “a reflection that the civil service has high standards and that people stick by the rules”. Nonetheless, he welcomes the commissioners’ move: “I don’t have a feeling at the moment that there is a big problem out there, but I do think it is right that the commission makes sure”.

However, Tony Wright MP, chairman of the public administration select committee, which is currently investigating Whitehall leaks, holds a less sanguine view. Wright has questioned whether civil servants can ever feel confident about complaining to their department; even commissioners, he noted during an evidence session with Paraskeva last week, take complaints back to departments and often name the whistleblower.

For civil servants to make allegations of breaches of the code “is not a career enhancing move”, Wright said. “It must be mightily difficult for a civil servant – even with a nominated officer; even with the civil service commissioners – to think that within the system they can get anywhere with this.”

This, a sympathetic Paraskeva argued, is precisely why an audit of the system is so important. “We surely don’t want to encourage a system where people don’t feel safe within it,” she said. “Our role is to make sure that the structures are there.”