Waiting-time guarantees have been broken on more than 1000 occasions in the past two-and-a-half years because NHS Scotland cannot cope with demand.
The problem seems to be growing, with the number of cases held up by staffing and resource problems growing year on year.
The Government insists the percentage of instances when targets have been breached has remained stable, but cancer charities and opposition politicians have expressed concern about the issue.
Under Scottish Government targets, patients urgently referred to hospital with suspected cancer should start treatment within 62 days and all sufferers should start treatment within 31 days of any decision to give them therapy.
Those who wait longer are given a code by NHS staff explaining the reason for the delay. Using the Freedom of Information Act, The Herald can now reveal hundreds of cases in which the codes show the main reasons patients waited too long were issues with facilities, such as lack of theatre space, or equipment failure, manpower problems – potentially due to unfilled vacancies – and staff holidays or sickness.
Last year, targets were breached 440 times due to a lack of theatre space or available equipment and 90 times because of staffing shortages. This represents a 41% increase on 2010, when there were 375 breaches as a result of service issues.
Figures so far this year suggest the number is going to rise again. In the first six months of 2012 there were 290 breaches caused by the same two problems.
Health boards are not obliged to hit the Government's cancer target 100% of the time, as there is a 5% tolerance because in some cases it is not medically appropriate for patients to be treated promptly.
However, The Herald's investigation shows staff and resource shortages account for more than half of all breaches, not the complexity of the cancer or the need for extra diagnostic tests.
Audrey Birt, Scotland director of Breakthrough Breast Cancer, said: "We know that waiting for a cancer diagnosis is a very anxious time for people. It is a concern that more than half of these delays are due to resource issues, especially as nearly 4500 women in Scotland are diagnosed with breast cancer every year. It is important the service has the resource to deliver quality care."
Health boards have had to battle with tighter budgets in the past two years and thousands of posts have been axed.
Jackie Baillie, health spokeswoman for Scottish Labour, said: "You can't keep cutting resources and staff and expect the NHS to perform more operations.
"That the NHS is responsible for hundreds of Scots having cancer treatment delayed is shocking.
"That isn't the NHS that we want to have in 2012."
The insight into waiting-list breaches comes just weeks after The Herald revealed how staff adjusted waiting-list results to filter out delays caused by failed diagnostic tests and clinicians changing their minds about treatments.
A Scottish Government spokeswoman said: "The percentage of patients breaching targets has remained relatively stable at around 5% or less since 2010, as more than 1000 more patients per quarter are now included under each of the cancer waiting times targets compared to early 2010."