The warning comes after the Scottish Government revealed more than 430 women were incorrectly excluded from cervical screening in the past 24 years, leading to the death of one woman.
A routine audit of cervical cancer data discovered in December last year that some women had not been invited for screening after a partial hysterectomy, when only those who had had a full hysterectomy should have been excluded.
Opposition parties criticised the government for not acting quickly enough to make the cervical screening error public, after ministers were informed about it in March.
This error was not caused by Covid-19, but it shows the potentially fatal consequences of problems in screening and treatment, Macmillan said.
As in that case, the impacts of the pandemic on cancer outcomes are likely to surface in several years’ time, said head of advocacy Kate Seymour.
Cancer charities have warned throughout the pandemic of a backlog in screening, diagnosis and treatment. There are thought to be 7,000 “missing” or undiagnosed cancer cases in Scotland
Opposition parties have repeatedly called on the Scottish Government to take more action to tackle the Covid backlog.
“There's a concern that with a delayed screening, people could be diagnosed later, which ultimately could mean people are diagnosed at the stage when their cancer can't be cured,” said Ms Seymour.
“It could also mean they're diagnosed at a late stage, which means they have to have more complex treatment.
“We know principally that surgery was stopped during the pandemic, so cancers that would have been best treated by surgery were treated in other ways.
“There is that concern that people may not have the same survival chances as they would have had if they had been treated early on with surgery.”
The 7,000 missing cases are a “real worry”, she said.
“Some of them will have gone through the other routes, but it’s undoubted that there are thousands of people who we would expect to have had a cancer diagnosis who haven't, and those inevitably are going to be the most vulnerable,” she said.
“They're going to be the people who end up being diagnosed perhaps through A&E at a later stage."
Ms Seymour said the impacts of delayed diagnosis and paused treatment would “go on for years”, pointing to the error around cervical screening, which began more than 20 years ago, but has only just been discovered.
“What we expect is that the progress that's being made on diagnosing people with cancer earlier is going to slip back,” she said.
“The impact of that is people having to have more invasive treatment or more impact of the cancer.
“And ultimately, we do think that it will mean some people lose their lives.”
She added: “We don't know yet what the impact will be, but there is going to be an impact. You can't have a pandemic and it not have an effect.
“It might end up not being loads and loads of people, but it will have an effect, and there will be people whose outcome of survival is not what it would have been if we had not had the pandemic.”
In reference to the one woman who died of cervical cancer following the screening error, Ms Seymour said the emphasis should be on preventing every death possible.
“Just because it's not 1,000 people or 500 people, it doesn't not matter,” she said.
"Everything that we want to do is for individuals, it is the job for people to make sure they get their best treatment and their best outcomes.”
In order to combat the backlog in diagnoses and treatment caused by Covid-19, these activities must get back to more than pre-pandemic levels, she said.
The same as before is “not good enough”, she said, “because we’ve got to catch up”.
The Scottish Government laid out a cancer recovery plan at the end of last year, including an investment of £114.5 million.
Patients are “at the heart” of the plan, the government said, and patient safety and the NHS are the “priority” ministers.
The plan included the set up of early cancer diagnostic centres, which recently opened in Ayrshire and Arran, Dumfries and Galloway and Fife.
Women’s health minister Maree Todd had earlier admitted more women may have been affected by the error in Scotland’s cervical screening programme than NHS Scotland was so far aware of.
Speaking to BBC Good Morning Scotland on Friday, Ms Todd said the true figure of those affected “may be higher”.
She said: "I'm afraid we may well be looking at higher numbers."
The records of at least 500 women who had partial hysterectomies before 1997 still need to be checked, Ms Todd said.
These are more difficult to access, but should be checked before the end of July.
Ms Todd said the NHS would review the records of all women who had been excluded because of a hysterectomy – some 200,000 people – as a “precaution".
But she “fully expects” there to be no further errors.
Opposition MSPs have questioned the delay between ministers learning of the issue and it being announced to the public.
Labour’s Jackie Baillie said: “The SNP’s decision to keep the public in the dark on such a serious mistake beggars belief.
“These women were failed for decades. The least they deserve is to have been made aware of the risk facing them as soon as it came to light.”
The Scottish Conservatives’ Annie Wells said: “SNP ministers have serious questions to answer as to how urgently they addressed this issue.
"They were first made aware of these errors in March well before Parliament shut down for the election, but only started sending out letters to women this week. That is simply not good enough."