Steve House, Chief Constable of the new Police Service of Scotland, warned of a "gobsmacking major problem" with the legislation setting up the force, which may deprive him of control over thousands of civilian support staff.
He remains locked in a dispute with Vic Emery, the chairman of the overseeing Scottish Police Authority (SPA) , who wants the body to be clearly responsible for civilian staff and force finances.
The two men appeared together at Holyrood's justice committee yesterday as MSPs tried to resolve the turf war.
Both men said they had taken independent legal advice in a bid to clarify their responsibilities under the Act which created the new force, but they admitted major differences still exist.
They insisted their disagreement was "healthy" and would ensure both the police and authority were properly accountable. But Labour MSP Graeme Pearson, a former senior police officer, described the situation as a "shambles".
Both the Chief Constable and the Police Authority – set up to fund and monitor the force – say they should control civilian staff and the finance department. They have so far failed to agree where new finance and human resources directors should be based.
Mr House told MSPs: "I absolutely believe it is essential I have day-to-day control of human resources and finance functions within the police service."
He added: "I did get legal advice. I did it after a conversation with the Strathclyde lead lawyer, because he alerted me to his concerns about the Act in a specific area. He didn't believe that the Act allowed the Authority to delegate to me control over support staff, which is clearly a bit of a gobsmacking major problem with legislation as far as I was concerned."
The two have agreed that the authority will control IT, audit checks on police spending and procurement, though Mr House will set out specifications for cars and other equipment.
The police and the authority will have their own press office and legal department. Mr Emery told MSPs: "You should be comforted we are having this debate now and are going to get it right."
But Mr Pearson, who headed the Scottish Crime and Drug Enforcement Agency, said after the meeting: "The SNP has created a single police force and an oversight authority which don't even know their respective roles.
"As a result, you have the Chair of the Authority fighting it out with the Chief Constable over who should run what, given that the legislation needs lawyers to tell experienced police figures what they can and can't do."
Mr Pearson added: "This is a shambles of the highest order, and to watch the total confusion in front of MSPs was bizarre, particularly given there are only four months left to build the new service.
"Kenny MacAskill created this mess – he needs to roll up his sleeves and help sort it out."
David O'Connor, president of the Association of Scottish Police Superintendents, who has backed Mr House in the row, said: We want the SPA to hold the Chief Constable to account but there is a need for clarity. We would urge parliament to find a solution."
A Scottish Government spokeswoman said: "Our legislation clearly sets out the roles and responsibilities of the Chief Constable and the Chair.
"It is for the Chief Constable and the Chair of the SPA to determine how best to fulfil their responsibilities."