Labour for Independence, one of the ad hoc yes campaign groups which sprang up in the run-up to last year’s Scottish referendum, is under investigation by the Electoral Commission for failing to file its accounts.

The commission – which is due to publish the full accounts for the two main referendum campaigns, Yes Scotland and Better Together, later on Thursday – started the inquiry on 29 April after prosecutors at the Crown Office (COPFS) decided they would not take action against the group.

The commission disclosed in February that Labour for Independence, a group called the Scottish Jacobite party, two individual campaigners and another yes vote campaign, the pro-independence blog Wings Over Scotland, were under investigation for failing to submit spending returns.

The Labour for Independence and Wings Over Scotland files were handed to the Crown Office. It is still reviewing the Wings Over Scotland case and it refused to comment on its progress.

Labour for Independence, which stated it was set up by and for Labour members in protest at the party’s decision to oppose a yes vote, ran into repeated controversy because of its close links to the Scottish National party.

While it included and was run by Labour members, SNP councillors and activists had posed with Labour for Independence banners and appeared on leaflets without making their party allegiance clear.

The commission said on Wednesday: “The Labour for Independence matter is now under investigation in line with our enforcement policy. Labour for Independence has failed to submit a campaign expenditure return as required by Schedule 4, part 3 of the Scottish Independence Referendum Act 2013 (SIRA).

“After consulting with the COPFS in order for them to consider whether they would open an investigation into this matter, they have decided not to take it forward and the commission has opened an investigation.”

Deborah Waters, a Labour for Independence committee member, told the Guardian she was unaware of the commission’s latest decision but claimed the group was able to submit full accounts. She said the group had received and spent a little over £10,000 during the campaign.

It had problems last autumn after a bookkeeper fell ill and was not able to use the commission’s online accounts reporting system in time, she claimed.

She added: “The financial records from the referendum are available and as soon as can be arranged, they will be with the Electoral Commission.”