The SNP administration approved a five-year deal for the Scottish Police Authority (SPA) headquarters to be at Bremner House in Stirling.
However, serious doubts hang over the move, which is now described as only an "option" due to potential IT costs and questions over the size of the organisation. A U-turn could cost the taxpayer more than £100,000.
Labour MSP Graeme Pearson, a former senior police officer who was director general of the Scottish Crime and Drug Enforcement Agency, said he feared the problems could cause an "obscene waste of public money".
The move to a single police force has been fraught with teething problems. Top of the list has been a power struggle between Police Scotland, the new force led by Stephen House, and its watchdog, the SPA.
The two sides battled for months about which had control over a range of corporate functions, which finally led to an uneasy truce.
The row over the scope of the SPA now includes its location. In October, just weeks after the interim SPA was set up, the SNP Government pushed ahead with a deal to base the body in Stirling.
The five-year lease, signed by a senior civil servant in the Justice Department, will cost £52,850 per year for more than 5000sqft of office space.
However, the SPA's range of corporate responsibilities has since grown and Bremner House is also not "cabled up" to receive sensitive police information.
A police service source said: "The SPA does not know whether it is going to be using that building. It needs to share information securely and there's a fundamental investment question to that."
The source added: "The SPA also needs to know the ultimate shape of the organisation. We thought it would be a secretariat, but it now has functions such as HR and finance."
The interim SPA is presently based at Elphinstone House in Glasgow, which is linked to the police network. Questions are also being asked internally about why the SPA needs another building, given that it is trying to rationalise properties across the police estate.
According to the lease, the deal can be terminated after two years, which suggests the taxpayer would foot a £105,700 bill even if the SPA do not move in.
The confusion will raise further questions about whether the Scottish Government prepared adequately for the introduction of the single force.
Cancelling the Stirling move could also trigger a backlash among MSPs who fear the new force will have a west of Scotland bias.
Pearson said: "When more than 1000 staff are facing redundancy across the service, it is an obscene waste of public money by this SNP government to carelessly lease a building that only months later could be deemed surplus at a loss of over £105,000.
"We have repeatedly asked the SNP government for evidence of its detailed business plans. It is about time Mr MacAskill [Justice Secretary] came clean."
An SPA spokesperson said: "We are considering what our ultimate headquarter needs will be. Bremner House is clearly an option, but we will require to complete our discussions with the Police Service of Scotland over the allocation of business activities before a full case can be considered."
A Scottish Government spokesperson said: "To ensure best value for the public purse and reduce the long-term liability for the property, the Scottish Government negotiated a five-year lease for the SPA's interim headquarters with several options to break the lease before the point negotiated into the contract."