The project was to be 4.5 kilometres east of Atlantic City in state waters and consist of six turbines. If approved, it would have been the first grid connected offshore project in the US.
The PUC has rejected the project on the grounds the state would be liable for up to $19.2 million if project funding through federal grants fell through. The total cost of the project would be $200 million.
Fisherman's Energy said it would "continue to work with the PUC" to develop the project.
In 2011, Fisherman's Energy, which is backed by commercial fishing firms, applied to the state Board of Public Utilities (BPU) for approval under new rules governing offshore wind.
The BPU had introduced the offshore wind renewable energy certificates programme, which will require projects to demonstrate a positive net economic impact on the state.
The second phase of the New Jersey project, planned to follow the demonstration phase, would be seven miles off the coast and have 66 turbines with a capacity of about 330MW.