Unison claims it has "absolutely no confidence" the civilian workers it represents will know whether they are working for the Police Service of Scotland Authority or its watchdog, the Scottish Police Authority (SPA), come April 1.
It follows a dispute between the new chief constable, Steve House, and SPA chairman Vic Emery over who should control the human resource function.
Justice Minister Kenny MacAskill had to step in to resolve the spat, encouraging both sides to share the role – a move which they eventually agreed to.
Each body will now have its own HR director, but it remains unclear which staff will be working for which organisation.
Gerry Crawley, Unison's lead police negotiator, said: "Seven weeks to go and thousands of support staff in Scotland still don't know who their employer is going to be, who they're going to be reporting to or where they're going to be placed.
"It certainly doesn't fill support staff with confidence.
"It's an absolute disgrace when there is so little time left to sort it out."
He added that the preference of Unison and its members is for workers to be under the remit of the chief constable.
There are currently a total of 6700 police support staff throughout Scotland.
It is understood 1200 employees who currently work for the Scottish Police Services Authority (SPSA) will automatically transfer over to the SPA.
However, it remains unclear how the rest will be divided up.
Mr Crawley added: "The SPA are more concerned with approving an HR director, a finance director, and a legal team, than deciding what will happen to these vital support workers.
"We have a meeting planned with the Justice Minister and we plan to raise this issue directly with him.
"The view at the moment is the SPA, through Vic Emery, are simply empire building."
A spokesman for the SPA claimed plans are under way to establish which employees will be covered by each body ahead of April 1.
However, he added that a full consultation process cannot take place until the new force is in place.
The issue comes following concern over who will hold the SPA to account amid fears it is not following proper public sector employment procedures.
Both Unison and the Association of Scottish Police Superintendents said there were questions to be answered over who keeps watch on the watchdog.
The SPA spokesman said the body's own board is responsible for ensuring its accountability.