But the defendant was a contractor of the organisation as the sole director of AGS Services and the services he provided were taxable.
Judge Grant Fraser said there was an "inevitability" about the outcome of Swney's sentencing in April but it might get worse for the disgraced entrepreneur.
The IRD charges come with a maximum penalty of five years imprisonment and/or a fine of up to $50,000.
When the charges were initially laid, a summary of facts filed by the IRD alleged Swney had issued "various fictitious invoices" to Heart of the City.
Investigators interviewed several organisations - including the Herald - over the authenticity of the invoices and determined they were created "without authorisation".
Swney is also on the end of a civil action launched by Heart of the City, whose board announced the move last month after accountants scoured their finances.
At court on Wednesday the defendant's lawyer Murray Gibson said they hoped to have everything dealt with on the April sentencing date.
"It's in the best interests of everyone that all matters get resolved at the same time."