When Nicola Sturgeon became Health Secretary in May, one of her first acts was to send in troubleshooting teams to tackle long waiting times for cancer treatment in NHS Lanarkshire and NHS Lothian. This was because she professed herself "appalled" that these areas were so far behind the target that 95% of urgent cancer patients should begin treatment within two months of being referred by their GP.

It was welcome recognition that early diagnosis and treatment is a vital factor in a successful outcome for cancer patients, and also that sharing expertise can lead to improved performance throughout the country. With Scotland as a whole at 10% below the target of 95%, Ms Sturgeon made meeting the target by the end of this year a priority. Today, however, it becomes clear that even if that target is met, hundreds of cancer sufferers will have to wait much longer. Figures obtained by The Herald under the Freedom of Information Act show that the system of referral which requires GPs to label patients as urgent or non-urgent results in some cancer patients being on the non-urgent list.

Of course urgent cases should be given priority; the problem is that GPs must decide whether a case is urgent or not before diagnosis. In many cases their judgment, based on a general examination and evaluation of risk factors, will be correct, but our figures show that, every year, well over 1000 people who were not urgent referrals were diagnosed with breast and bowel cancer alone. The discrepancies between the urgent and non-urgent patients were particularly marked for bowel cancer patients, with the non-urgent cases having to wait from seven to 16 weeks longer in different health boards.

We know that with bowel cancer earlier treatment is more effective, and that once patients are diagnosed with cancer they all have equal access to treatment; the problem is getting the diagnosis. The new bowel cancer screening programme, which should be available throughout the country to people over 50 by the end of 2009, will identify potential cancer sufferers at an earlier stage. Inevitably, however, that will lead to the need for further investigations, putting further pressure on the system. The problem is stated succinctly by Professor Malcolm Dunlop of Edinburgh University and the Western General Hospital: "There are not enough colonoscopists and there are not enough pathologists." There is a further difficulty. While the divide between urgent and non-urgent has revealed the hidden waiting lists of the yet-to-be-diagnosed, there is another group hidden deeper in the statistics: those with non-cancerous but painful conditions who need the attention of the same specialists.

The major problem facing the NHS is how to make the most effective use of limited resources with demand always stretching its budget and its staff. Setting targets is a way of prioritising cases, but it can sometimes be too crude a mechanism. In this case it could be refined by more accurate referrals from GPs. They should continue their referrals audit, but the targets themselves should also be audited for effectiveness.