Public Health Scotland said the decrease was not in line with long-term trends and was likely to be due to under-diagnosis.
A pause in screening services because of Covid also meant cancers were detected later, the report said.
Macmillan Cancer Support said the figures were "shocking".
The report said Covid had a huge impact on all aspects of cancer control in Scotland, causing widespread disruption from the end of March 2020.
All cancer screening programmes were paused for several months and urgent referrals for suspected cancer fell substantially, it said.
Patients were less likely to seek help and delays in investigations may have led to patients not being diagnosed in 2020 when they could have been, according to the report.
Treatment And Support
Figures in the report show a 9% drop in the number of cancers diagnoses from 33,156 in 2019 to 30,395 cases in 2020.
The four most common cancers in Scotland all showed a fall in the numbers diagnosed - lung (down 7%), female breast (down 11%), prostate (down 10%) and colorectal (down 19%).
The report said that pausing screening services led to an under-diagnosis of the early-stage breast (-20%), colorectal (-33%) and cervical (-45%) cancers compared with 2019.
Peter Hastie from Macmillan Cancer Support said delays in diagnosing cancer can lead to people facing more serious treatments or to the disease being at a stage which can't be treated.
He said: "Even before the pandemic, the system was struggling with the sheer numbers of people in need of treatment and support.
"There are immense pressures on the NHS and its staff, and it's vital it has everything it needs to diagnose and deliver vital care to people living with cancer. "
The Scottish government's public health minister Maree Todd said the NHS remained under sustained pressure as a result of Covid, with the number of people awaiting diagnostic tests now at the highest level since 2018.
"Patients continue to be seen based on their clinical urgency, for example those referred with an urgent suspicion of cancer continue to be prioritised for key diagnostic tests," she said
"Significant funding has also been targeted at increasing diagnostic capacity across NHS Scotland."
Scottish Conservative public health spokeswoman Sue Webber said the figures were the latest evidence of a cancer "ticking timebomb" in Scotland.
"The pandemic has clearly been a big factor here, but the SNP have been failing on cancer detection and treatment since way before Covid," she said.
Ms Webber called for the health secretary to provide the NHS with the resources to to get on top of the crisis before more lives are lost.
Scottish Labour accused the Scottish government of "dangerous complacency" for failing to put in place a proper catch-up plan in the aftermath of the pandemic.
Scottish Liberal Democrat health spokesman Alex Cole-Hamilton said the Scottish government needed to get a grip on cancer care and treatment as a matter of urgency.