The Scottish Government has paused certain cancer screening programmes to free up healthcare staff in response to the coronavirus pandemic.
But Jeane Freeman said core treatments such as urgent surgery should be protected, despite the outbreak.
"These are particularly difficult times and we understand that patients undergoing treatment for cancer will feel especially anxious," she said.
"Our NHS boards are working hard to ensure vital cancer care remains and I have written to all health boards outlining my expectation that all vital cancer services continue."
She added: "Many medical procedures do now carry a far greater risks due to Covid-19.
“Because of this, other treatment plans may be proposed and discussed with patients.
"Patient-facing guidance has been developed and distributed via cancer services across Scotland to provide advice for people with cancer about how Covid-19 might affect them."
The 200,000 people living in Scotland who are most vulnerable to Covid-19 are also being offered extra support, such as food and medicine.
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