DISQUIET about the functioning of Holyrood's committees has been growing for a while but only today have Hugh Henry, Duncan McNeil and Michael McMahon stuck their heads above the parapet.

The system is "no longer fit for purpose", they claim. The key role of the committees – to hold ministers to account and improve legislation – has been closed down by a controlling SNP machine that is using its backbench MSPs to suppress the merest whiff of criticism of the Government. Labour's elder statesmen accuse them of blocking potentially embarrassing inquiries, refusing to call difficult witnesses and generally stitching up business in private sessions away from the prying eyes of the press and public.

It is a serious complaint that raises troubling questions about the health of Scottish democracy. But it is not surprising it has taken so long to bubble over in the public domain. Private business in committees is, well, private, and MSPs – especially conveners – are aware of their duty to respect that. What's more it is never pleasant for anyone to admit they are powerless (which Labour are at Holyrood) and being pushed around (which is how the party's MSPs feel).

On top of all that the SNP have a simple and crushing rejoinder readily to hand: this is all just sour grapes from a bunch of bad losers. Previous Labour-LibDem administrations had an in-built majority on the committees and now it is the Nationalists' turn. "Deal with it," I can hear Jamie Hepburn thinking. The now-unprotected heads of Messrs Henry, McNeil and McMahon are there to be shot at.

And yet. The slow drip, drip of leaks from behind-closed-doors committee meetings continues and the muttering in corridors grows louder. What if there is a genuine problem here? We would all be unwise to ignore it. Unlike Westminster, Holyrood has no second chamber to send ministers away to think again. If Scotland is to have sound laws, if ministers are to govern well, if public bodies are to do their jobs properly, it is largely down to the committees. Their importance in Donald Dewar's streamlined system cannot be over-stated.

Margo MacDonald, the only independent MSP and a fierce defender of the institution of parliament, believes the committees have always been prey to party politics. It's the way of the world, she says, and she is surely right about that. But she is concerned that the massed ranks of backbenchers elected in the SNP landslide last year are less conscious of their wider role as parliamentarians than previous intakes. New MSPs, eager for promotion, tend to do what they are told. Factor in the referendum race and it's easy to see why party whips have the upper hand.

There are honourable exceptions. No-one would (dare) accuse the redoubtable Christine Grahame of bringing anything less than a spirit of independent thought to her convenership of the justice committee. Stewart Maxwell, at education, has also won praise. They are probably the closest Alex Salmond has to an awkward squad, however, and, even then, on an awkward-ometer scale of one to 10, they score about six.

From Labour's point of view the committee problems are part of a pattern – and they are determined to exploit them. Johann Lamont seized gleefully on former SNP deputy leader Jim Sillar's description of his party as "totalitarian" and she stayed on the theme at First Minister's Questions this week, claiming Mr Salmond was running Scotland "like North Korea".

That's all good knockabout stuff but it is unlikely to solve a tricky constitutional conundrum. We need a proper debate on whether Holyrood is broke and, if so, how best to fix it. As Mr McNeil says, if the committees are not fit for purpose now we are storing up problems for the not-too-distant future. Half your income tax will be set at Holyrood in 2015, and you wouldn't want that to be going on without a robust, well-informed debate, would you?