Alex Neil said those areas which are failing to treat patients within 62 days of urgent referral would be given "additional advice".
The latest figures show that for the period October to December last year, five boards - NHS Grampian, NHS Highland, NHS Tayside, NHS Lothian and NHS Greater Glasgow and Clyde - did not achieve the target.
Three of these boards, NHS Grampian, NHS Highland and NHS Greater Glasgow and Clyde, also failed to meet the treatment time target for the previous three months, according to official statistics.
In NHS Tayside, 90% of patients started treatment within 62 days of being urgently referred in October to December, while only the three island health boards, NHS Orkney, NHS Shetland and NHS Western Isles, treated 100% of patients within this time.
Across Scotland as a whole the target was missed, with 94.6% of people starting cancer treatment within two months of being referred.
The target was not met for all cancer types either. While 98.8% of breast cancer patients began treatment within two months of being referred, only 89.3% of melanoma skin cancer patients started treatment in this time, as well as 90.7% of those with head and neck cancers and 91.3% of lung cancer sufferers.
The standard was also not met for colorectal, lymphoma, and urology cancers.
Mr Neil said: "While NHS Scotland provides some of the best cancer care in the world, we scrutinise waiting times performance because patients should not suffer unnecessary distress because of lengthy waits for a diagnosis or to start their treatment.
"We are monitoring on a weekly basis those health boards who are not regularly meeting the 62-day cancer standard and a support team is visiting boards to offer additional advice. I believe that this group will bring about real improvements and help health boards to ensure that these key targets will be met in the future."
Across Scotland the target for having cancer patients start to receive help within 31 days of a decision being made to treat them was met, with 97.9% of people beginning treatment within this time in October to December.
"The quality of cancer care is something everyone cares deeply about and the Scottish Government will do everything it can to make sure that all patients and their families get the support they need," Mr Neil said.
"This includes ensuring that those requiring urgent treatment have swift access to specialist services which has resulted in almost 98% patients start treatment within 31 days of a decision to treat between October and December 2013.
"We are doing all of this because we know that the earlier cancer is detected and treated, the greater the chance of survival. We have set ourselves the ambition to increase early detection and raise Scotland's cancer survival rates. We continue to tell the public 'don't get scared, get checked' and will do everything we can to ensure that once they get checked they are treated as quickly as possible."
Labour health spokesman Neil Findlay said: "The bottom line is that people are still waiting too long from referral to receiving their first treatment. The Health Secretary, Alex Neil, has not done enough to ensure that targets are being met.
"The rationale for targets should not be to provide a baseline on how health boards are performing but to provide patients, who are going through a horrendous experience, to get the action they need to aid in their recovery.
"Now Alex Neil thinks that sending in 'support squads' will do the job. But it's no coincidence that the health board areas who are struggling the most to meet targets cover the most populated areas of the country. They need resources to help them manage the increasing demands of patient care, not an extra layer of bureaucracy."