The project's head contractor Contract Control owes its subcontractors several million dollars for work on the theatre. 

Contract Control director Stefan Seketa said the payment hold ups were a result of unapproved variations to contracts.

He said it may take several months for subcontractors to be paid in full. 

"There are a number of variations still being worked through," he said.

"Suffice to say it's an ongoing issue and will be resolved in the fullness of time.

"It's a process we've got to work through. It's regrettable."

He said the state education department - which is footing the bulk of the bill for the theatre - was committed to working through the variations. 

"Where variation money has been paid, it has gone through to the subcontractors," he said. 

Mr Seketa said no subcontractors had walked off site. 

Contract Control has been responsible for several big ticket public projects in central Victoria including the Bendigo Library redevelopment. 

It has also been awarded the contract for the Boort Hospital redevelopment.

A separate contractor said his company was owed more than $100,000 by Contract Control for work on Ulumbarra from payments due back as far as November. 

A company spokesperson said similar problems had arisen on other Contract Control-run projects, including the library redevelopment.

"We've worked with them on different sites and their practices are the same on every site," he said.

The company is awaiting an adjudication from its claim against Contract Control through the Security of Payments Act. 

The spokesperson said the company would no longer work with Contract Control.

"We just can't afford to. It's not worth the emotional drain," he said.

"It makes it really tough. Cash flow is really important for a small business."

The spokesperson said it was disappointing that Contract Control continued to win contracts for government projects given its payment history. 

He said local and state governments should have provided more oversight to ensure workers were paid.

"We would've hoped given it was publicly funded, they would have made sure the contractors all actually get their money," he said.

The education department processed a payment to cover some of the contract variations June 12.

Contract Control agreed to pass on the payments to subcontractors by June 19.