The SNP has changed the way it records party donations and is now keeping documentation of all amounts under £250, the first minister has said.
It comes after the SNP’s new auditors flagged up an issue with its accounts.
Humza Yousaf said this was because the party previously only kept online records of donations under £250.
Auditors had made a “qualification” because of the missing paperwork, but the SNP said it was still on track to file accounts by the 7 July deadline.
The accounts will note that original records for some cash and cheques had not been retained for this and previous financial years.
The SNP said the issue was down to “administrative processes” and there was “no suggestion of misappropriation of funds”.
In an interview with PA news agency, Mr Yousaf said: “The qualification the auditors refer to is in relation to donations that are under £250, to ensure that we keep hard copy documentation of those donations.
“We do keep an online record of them, but the auditors say there should be a hard copy well.”
He added: “As soon as the auditors raised that issue with us, the treasurer Stuart McDonald made sure the party immediately took steps to keep hard copy records.”
On Friday, the first minister had declined to say how much money was involved in the missing documents.
The SNP had to find new auditors when the Johnston Carmichael firm quit last September, although it was not made public by the party until this year.
AMS Accountants Group was later appointed to take on the job.
Mr Yousaf said at the time there had been a “significant amount of doubt as to whether we would get those accounts submitted on time”.
The SNP remains at the centre of an ongoing police investigation into its finances and funding.
This has seen officers arrest former first minister Nicola Sturgeon, her husband Peter Murrell – the party former chief executive – and former treasurer Colin Beattie.
All three were subsequently released without charge pending further investigation.
The police inquiry centres on what happened to more than £660,000 of funds given to the party by activists to be spent on a future independence referendum.