New Public Health Scotland (PHS) figures indicate a cancer diagnoses confirmed through a tissue sample fell by around 4,000 between March and June compared to the previous year - a drop of about 40%.
PHS said the fall is "unlikely to be due to a reduced occurrence of cancer".
It added the reduction is likely to reflect a combination of patients with possible cancer symptoms not visiting their GP perhaps over coronavirus fears, changes to the national screening programmes in the first few months of the pandemic, and less availability of diagnostic services and treatment during this period.
Cancer charities have raised concern about the figures, stressing early diagnosis and treatment is lifesaving.
Macmillan head of policy in Scotland Kate Seymour said: "These figures are extremely worrying. A 40% drop in diagnoses is staggering.
"Delays in diagnoses can lead to unnecessary deaths, as well as people facing more serious treatments that leave them with long-term health issues.
"The Scottish Government must ensure the cancer care system has the resources to diagnose and treat thousands of additional people, many of whom may have more advanced cancers than would normally be expected due to the delays.
"The Government must also launch a widespread public awareness campaign urging anyone with cancer symptoms to contact their GP."
Marion O'Neill, head of external affairs at Cancer Research UK, echoed this call and urged the Scottish Government to address the backlog of tests, saying the pandemic has had a "devastating" impact Scotland's cancer services.
She said: "Early diagnosis followed by swift access to the most effective treatment can be lifesaving.
"We're concerned that even if people are going to the GP, if they are not receiving follow-up diagnostic tests in good time, many more cancers will be diagnosed at a late stage when they're harder to treat."
Professor David Morrison, director of the Scottish Cancer Registry at PHS, said: "The reduction in cancer diagnoses this year gives us a sense of the scale of the impact of Covid-19 on all stages of the journey from first seeking help to recovering from treatment.
"If you're worried you might have cancer - see your GP and get checked out. It's probably not cancer - but if it is, the sooner you're diagnosed, the better your chances of successful treatment."
Questioned on the figures at the Scottish Government's coronavirus briefing, both Nicola Sturgeon and deputy chief medical officer Dave Caesar urged anyone with concerns to see their GP.
Asked if the figures indicate the coronavirus restrictions on screening and cancer treatments have possibly caused more harm than good, the First Minister said that is not the case, and added: "Without those restrictions we would not be facing, as we are, the already grim death toll of 5,000, it would be many, many, many times that, potentially, but we've always acknowledged that lockdown restrictions do other harms which is why we have the harm analysis of any restrictions that we have."