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Auditors for the Scottish National party, whose finances are being investigated by the police, have flagged an issue with the SNP’s accounts because of missing documents about membership fees and donations.

AMS Accountants, which was appointed after the SNP’s previous auditors quit, had issued a qualified audit opinion on the accounts for 2022, the party said on Friday.

The disclosure will intensify scrutiny of the pro-independence SNP’s finances amid a police investigation that led to the arrest of Nicola Sturgeon, Scotland’s former first minister and former party leader, in June.

The SNP has been plunged into crisis by the police probe that was sparked by complaints that more than £600,000 raised from independence supporters for a referendum was used for other things.

AMS said the SNP had failed to keep original records of “some items of cash and cheques” from 2022 and 2021 relating to “membership, donations and raffle income”.

This meant that AMS was “unable to determine whether any adjustment to income is necessary” in the party’s accounts, added the auditors.

SNP treasurer Stuart McDonald said the party had “engaged with [the] auditors and implemented administrative changes in accordance with their recommendations” and that lessons from the process would be incorporated into an ongoing review of its governance.

The SNP said it was “on course” to meet a deadline to supply accounts to the Electoral Commission, the watchdog.

AMS was appointed as the SNP’s auditors in May after the party had struggled for months to find a replacement for Johnston Carmichael, which resigned from the role in October last year.

“The murkiness around the SNP’s finances just won’t go away,” said Craig Hoy, chair of the Scottish Conservatives. “This would amount to a shocking lack of transparency in any organisation. From a party in government, it is a disgrace.”

Humza Yousaf, who succeeded Sturgeon as first minister and SNP leader in March, has found his first few months overshadowed by the police investigation into the party’s finances.

In April police arrested Peter Murrell, the former SNP chief executive who is the husband of Sturgeon, and Colin Beattie, the party’s then treasurer. No charges have been brought against Sturgeon, Murrell or Beattie.

The SNP, which has dominated Scottish politics since winning power in Edinburgh in 2007, has in recent months suffered a decline in support, according to opinion polls.

Surveys suggest the SNP is in danger of winning fewer Westminster seats than Labour at the next UK general election.