Britannia Construction is main contractor on the job to build a six-screen Cineworld.
But a mix-up meant the main building is being erected 880mm closer to neighbouring homes in East Street than originally approved by planners.
The position of a separate building on the Huntingdon Street site has also been identified as 197mm out of place.
A new planning application has now been submitted to the council’s development management panel – with a decision likely to be made next month – and a full public consultation will also be launched.
Construction work has resumed in the mean time.
A district council spokeswoman told the Huntingdon News & Crier: “As a result of a complaint made to Huntingdonshire District Council, its planning enforcement officers have investigated the position of the new cinema building which is under construction.
“It has been found that the building has not been set out in accordance with the approved plans.
“This has been brought to the developers’ attention, and they have this week submitted a planning application to enable the council to consider whether planning permission should be granted for the building in the position in which it is being built.”
The 32,000 sq ft site will also contain four restaurants and a public plaza.
Developer Turnstone managing director Chris Goldsmith said: “This was a genuine mistake where the building was approximately one per cent closer to the homes in East Street than it should have been.
“Hopefully it will not cause too much of a delay to the project.”
Britannia started on site last December.
Other members of the project team are JWA Architects and structural engineer Mott MacDonald.