Seven boards failed to hit the standard for getting at least 95% of patients with a suspicion of cancer to their first treatment within 62 days.
NHS Grampian scored lowest with 89.5% and Orkney was the only board to hit 100%, according to the official statistics covering July to September.
The target was also missed by Greater Glasgow and Clyde, Ayrshire and Arran, Highland, Borders, Fife, and Shetland boards. The national average was slightly below the target at 94.5%.
All 14 boards passed a second target to ensure 95% of all patients, regardless of route of referral, wait a maximum 31 days from decision to treat to their first treatment.
In this case, the national average was 98.1%, up slightly on the previous figures.
Scottish Labour health spokesman Neil Findlay said it represented "hundreds of Scots left with an agonising wait to begin treatment".
He said: "Almost everyone in Scotland is affected by cancer, be it your own diagnosis or that of a family member, friend or colleague.
"Early diagnosis is improving in part because of years of campaigning from the marvellous cancer charities we have here. But more needs to be done to ensure quick access to treatment is available for all patients with all types of cancer.
"The treatment guarantee needs to be reviewed and lowered to give all patients the best chance of survival and we need to know whether beyond that people are continuing to receive follow-up treatment quickly because this is not currently documented."
Liberal Democrat MSP Jim Hume said steps must be taken to stop a "worsening crisis".
He said: "It is a grave reflection of the state of our health boards that half have missed the national cancer treatment target. There has been barely a jot of improvement this year.
"This will be upsetting for patients and their families, already coping with the stress of a loved one being diagnosed with cancer. Sixty-two days alone must feel like decades, which is why the Health Secretary must get a grip of this unacceptable situation."
Health Secretary Alex Neil said 4000 more patients had been treated under the 62-day standard since 2007.
He said: "We understand that having to wait for tests or to begin treatment can be frightening and, at the very least, frustrating.
"That is why we continue to scrutinise performance across NHS Scotland and request action plans from NHS boards where performance against the cancer waiting times standard has not been maintained.
"When it comes to cancer, we are determined to take all the necessary action to improve earlier diagnosis, advance the treatments available to patients and invest in staff and equipment."
The statistics came as new analysis from Cancer Research UK showed death rates from the disease had dropped almost a fifth in just over two decades.
The charity said the number of people in every 100,000 who died from cancer fell to 196 in 2011. That is an 18% decrease from the proportion in 1990, despite an ageing population meaning more people are being diagnosed with the disease.
Over the same period, the cancer mortality rates for men and women fell 23% and 15% respectively.
Mr Neil said: "The simple truth is, more people are surviving because treatments are better and more people are getting checked earlier.
"The earlier cancer is found, the easier it is to treat and the more likely you are to survive.
"That is why we are telling the public not to get scared, get checked and why we will do everything we can to ensure that once they get checked they get treatment as quickly as possible."