Police have given staff at AFL House the all-clear to return to work after a threat was received on Thursday afternoon, sparking an evacuation of the organisation's headquarters.

More than 150 AFL employees in Melbourne's Docklands were forced to evacuate about midday after the league received a threatening phone call.

On Wednesday, the AFL changed its logo on the building to "Yes" in support of same-sex marriage but removed it by Thursday morning, claiming it was only a temporary measure.

Police declared the area safe after conducting safety checks, with staff returning to work shortly before 1.30pm.