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Yes Scotland Ltd, which was launched by former SNP leader and First Minister Alex Salmond to campaign for independence ahead of the referendum, has not been active since 2014.
Its latest set of dormant accounts were published last year, showing a zero balance.
Yes Scotland previously pointed BBC Scotland to the audited referendum returns which are available online.
Figures published by the Electoral Commission, external show that Yes Scotland reported receiving donations of more than £2.6m and spent more than £1.4m during the referendum campaign.
The pro-union Better Together campaign reported receiving almost £3.7m in donations and spent more than £1.4m.
Aamer Anwar said full sets of Yes Scotland accounts for 2013, 2014 and 2015 were voluntarily provided to Police Scotland on 13 July.
"To be clear, there is no 'missing' £1.5m," he said.
"But what is missing is any explanation as to why it did not occur to those making the allegations that the £1.5m represents spending by the campaign."
The SNP has said Yes Scotland Ltd was an "entirely separate organisation" from the party.
It comes after the party's former chief executive Peter Murrell was jailed for more than five years after he admitted embezzling more than £400,000 from the party over five years.
Police Scotland and the Crown Office investigated Murrell's actions in Operation Branchform.
