John Bourn, auditor general for Wales, made the admission in a letter to members of the assembly audit committee this week.
Bourn wrote: "This is a very complex and technical area, and the issues disputed by the assembly and the Richard Rogers Partnership may be subject to legal action."
The audit committee asked Bourn to make further inquiries about the scheme, which has been dogged by dispute after architect Lord Rogers was sacked in July after a dispute over costs. Rogers said last month that he wanted to be reinstated as the scheme's architect.
The letter was presented to the committee on Tuesday, along with an interim report on the scheme.