In June, ministers told MSPs hundreds of women were not invited for cervical cancer screening checks, but were criticised after it emerged they were informed of the issue in March.
However, documents show that similar issues around the recording of sub-total hysterectomies were first identified in June 2016 and led to two reviews into the cervical cancer screening programme around that time.
Documents sent to health boards state that officials blamed the exclusions at that time on software faults and human error.
Ministers are expected to give an update on the scandal to Parliament on Wednesday.
Scottish Labour, who obtained the documents using Freedom of Information legislation, accused the Scottish Government of taking its “eye off the ball” on the issue.
Depute leader and health spokesperson for the party, Jackie Baillie, said: “This is clear evidence of the SNP Government’s failure to protect the health and wellbeing of some of Scotland’s most vulnerable women – they must have answers.
“By taking their eye off the ball, the government has allowed the true scale of this scandal to be hidden for many more years than need be.
“Lives have been put at risk and tragically at least one life has been lost. This is not good enough.
“When the minister makes her statement to the Parliament this week, she must say why this scandal was not resolved when suspicions were raised so many years ago.”
NHS Scotland uses a piece of software called the Scottish Cervical Call Recall System (SCCRS) to administrate the cervical cancer screening programme.
Women are routinely invited for cancer screening unless they have had a total hysterectomy and therefore no longer have a cervix.
In 2016, the documents show, at least 29 women were “inappropriately excluded” by the system to a software “bug”.
A further review in 2017 showed a further 11 women were wrongfully excluded by the system.
NHS officials blamed “misuse” of the “no cervix” exclusion and also said some GPs had wrongly updated patient records which led to their exclusion.
One document sent to health boards states: “A number of errors were made in adding the initial sub-total hysterectomy information. These errors were in part down to human error and inadequate quality assurance checks at the lab, but also indicated problems with the lack of clarity regarding the hysterectomy type information provided from secondary care.”
Announcing the errors to Holyrood in June, minister for public health Maree Todd said the government would learn from the incident.
She said: “This incident will be profoundly worrying to many people. For the women and families whom I referred to at the beginning of my statement, it has had devastating consequences, and nothing that I say can undo that.
"However, I make the commitment today that everything that we do surrounding this incident will be guided by three principles.
"Our focus will be on identifying and providing the appropriate support and care for anyone who has been wrongly excluded. We will be open, transparent and welcoming of the scrutiny that this investigation rightly deserves, and we will learn from the incident so that it cannot happen again.”
A Scottish Government spokesperson said: “In the course of previous investigations into data discrepancies within the screening system, a number of incorrect exclusions were discovered. Every case identified at the time was rigorously reviewed and it was believed that all errors had been found and resolved.
“Since March 2021, our priority has been to review as quickly as possible the records of those who appear to have had subtotal hysterectomies and been wrongly excluded.
"However, given the incidents that have subsequently come to light, it is clear that we must also review whether opportunities were missed that would have allowed us to understand the full scope of the issue earlier.
“The Minister for Public Health, Women’s Health and Sport will update Parliament on this on Wednesday and the wider work to manage the issue of inappropriate exclusions.”