Amec and Garbe have entered into adjudication over cost overruns and delays to the refurbishment.
The news emerged as Garbe sold the building to a private Irish consortium for £160m this week.
An Amec spokesperson said that the project is now complete, 75% was let or occupied and that the firm was not aware of any substantial defects.
But he said: "However, a number of commercial matters remain outstanding with the client and we are trying to solve them amicably."
A project insider said completion of the project had been nearly a year late due to technical difficulties in construction.
He said: "The project is the first commercial project design carried out by Alsop. Amec appears to have found it more difficult than they expected working on such a complicated refurbishment of a grade-II listed building."
The insider also claimed there were defects on the project, such as problems with the coating on the pods, which are one of the most distinctive features of Victoria House's refurbished interior.
Amec has found it more difficult than expected working on such a complicated refurbishment
Victoria House project insider
He said: "The result was that Garbe has had to cover a great deal of additional cost on the project and was pursuing Amec by instigating legal action."
A Garbe spokesperson said: "The outstanding commercial issues are being dealt with in an orderly fashion commensurate with such a large and complex project."
It is also understood that there is legal action pending between Amec and subcontractors on the project.
The £160m sale to a private Irish consortium, which is a client of Allard Ryan Consulting and Clearwater Estates, is being completed this week. Victoria House was bought by Garbe for £28m in 1999.
The project insider added that Garbe expects its additional costs on the project to eat into any profits unless compensation from Amec is forthcoming.
Alsop's conversion of Victoria House for Garbe was his third design for the building; his first was in 1998, when Blackfriars Investments was considering Victoria House for the Greater London Authority.
Alsop also drew plans for a shopping centre for Garbe, which then switched to a speculative office development that has become home to Sport England and the Competition Commission.