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The SNP's new auditors have flagged up an issue with its accounts, the party has revealed.
Its treasurer said the SNP was still on track to file the necessary paperwork with the Electoral Commission on time.
But he said one "qualification" has been made by the auditors because of missing documents.
The accounts will note that the original records for some cash and cheques had not been retained for the current and prior financial years.
The records relate to membership, donations and raffle income.
The auditors will state in the accounts: "We have been unable to satisfy ourselves by alternative means regarding the completeness of income in respect of the above limitation in scope.
"Consequently we are unable to determine whether any adjustment to income is necessary in the current or prior year and the potential impact on opening reserves accordingly."
The SNP said the qualification was down to "administrative processes" and there was "no suggestion of misappropriation of funds".
It also said that administrative changes had already been made on the recommendation of the auditors and that "there is no suggestion that the accounts do not present an accurate picture of the party's financial position".
The information was outlined at a meeting of the party's National Executive Committee on Thursday evening, which approved the accounts for 2022.
Party treasurer Stuart McDonald said: "We have already engaged with auditors and implemented administrative changes in accordance with their recommendations and will continue to do so.
"Our learning from this process will also feed into the governance review which is under way, and which will see us adopt the best practice and procedures in terms of oversight."
The SNP had to find new auditors when the Johnston Carmichael firm quit after working with the party for more than a decade.
Johnston Carmichael informed the SNP of its decision last September, but it was not made public by the party at the time.
Humza Yousaf has said he only found that the party no longer had auditors in place after he won the contest to succeed Nicola Sturgeon as SNP leader in March.
Mr Yousaf announced at the time that the party would carry out a review of its governance and transparency.
The party initially struggled to find another auditor willing to take on the work, but eventually appointed Manchester-based firm AMS Accountants Group at the start of May.
AMS managed to submit accounts for the SNP's Westminster group to parliamentary authorities by the end of that month, which it needed to do to avoid losing up to £1.2m in public funding.
It must now file accounts for the party as a whole with the Electoral Commission in July.
The party is still at the centre of an ongoing police investigation into its finances and funding which has seen officers arrest Ms Sturgeon, her husband Peter Murrell - the party former chief executive - and former treasurer Colin Beattie.
All three were subsequently released without charge while further inquiries are carried out.
Mr Murrell had been the SNP chief executive since 1999 but quit in March after it emerged the party had given misleading information about its membership numbers to the media.
The Glasgow home of Ms Sturgeon and Mr Murrell was searched as part of the investigation, as was the party's HQ in Edinburgh, with several boxes seen being removed from both properties.
A luxury motorhome was also removed from outside the home of Mr Murrell's mother in Dunfermline.
The police inquiry centres of what happened to more than £660,000 of funds given to the party by activists to be spent on a future independence referendum.
Speaking after being released from police custody on 11 June, Ms Sturgeon said: "I know beyond doubt that I am in fact innocent of any wrongdoing."