Wide concerns about an initial return rate of 79 per cent saw the 2022 census extended by a month, increasing the rate to 89 per cent.
Officials say robust data can still be produced despite missing the target of 90 per cent and a minister has denied that poor communication was to blame.
Audit Scotland has now laid a Section 22 report before the Scottish Parliament, highlighting a matter of public interest regarding a public body’s accounts.
It noted the census in England and Wales concluded with a response rate of 97 per cent.
The report said NRS continues to investigate why the response rate in Scotland was lower than expected.
Extending the deadline is expected to cost an additional £6m, equating to around 4 per cent of an overall programme budget of £144.6m.
The report said “significant” work remains to be done to produce robust data and said NRS should be transparent about its process.
In September, the UK’s National Statistician Sir Ian Diamond said the census could still provide “really good” data despite a lower than expected return rate.
MSPs were told that administrative data was now being used to a greater extent than initially planned.
Constitution secretary Angus Robertson has said accusations of poor communication around the census “do not stand up to any fair scrutiny”.
Stephen Boyle, Auditor General for Scotland, said: “The census is a vital data gathering tool that allows public services to be planned properly.
“It’s important that National Records of Scotland establishes why the return rate was significantly lower than the other countries in the UK.
“Those lessons should be shared and will be crucial to planning for future censuses and surveys.”
Conservative MSP Donald Cameron commented on the Section 22 report, saying: “It was clear from the moment that the Scottish Government decided to hold their census on a different date from the rest of the UK that it would cause trouble.
“Now the Auditor General has confirmed that this led to increased costs and a worse response rate than any other part of the country.
“He’s right that lessons must be learned – and I would hope Angus Robertson has the sense to accept them.
“The first of these is that the SNP must never again allow manufactured differences to distort the proper conduct of government business, wasting public money in the process.”
Householders had initially been warned those who did not return the census may be prosecuted, with potential fines of as much as £1,000.
Nicola Sturgeon had been forced to personally defend Scotland’s census as a "credible exercise" when details of the lacklustre initial response rate emerged.