Police raided the offices of Sage and mining company Cape Lambert Resources in the inner-Perth suburb of West Leederville and also in Sydney, as part of an ongoing tax office investigation.
The offices are also headquarters for the Glory, but on Thursday the club released a statement declaring they were not the target of the raids.
The West Australian-based A-League club also revealed that the police had not entered the Glory offices.
"Perth Glory Football Club is aware of statements from the Australian Federal Police, together with associated media coverage, concerning the execution of warrants at a number of locations in Perth and Sydney," the statement said.
"Perth Glory, which is within an office complex shared with other non-related companies, was not served with a warrant, nor was its office entered by the authorities.
"It believes the matters relating to the execution of these warrants are not related to its business in any way.
"Perth Glory will be making no further comment on this matter and is looking forward to tomorrow night’s game away to Brisbane Roar."