If a disagreement arises with your local authority and/or your Full Plans are rejected, there are a number of different options open to you.
The simplest way to proceed if your plans are rejected is often to re-submit your Full Plans application with the suggested amendments, in order that a Notice of Approval can be issued. You will then have the benefit and protection of having your Full Plans approved. You also might not have to pay any additional charges.
If you disagree with the council's view and believe that the plans submitted do comply with the Building Regulations and do not need amending, you can refer the matter (in England) to the Department for Communities & Local Government.
You will need to ask for a determination as to whether or not your proposals comply with particular requirements in the Regulations. You can ask for a determination before or after the Council gives a formal decision on your plans, but this can only be done before the work has substantially started.
If you believe a particular requirement of the Building Regulations is too onerous or inappropriate to the particular circumstances of the work, you can ask the Council to relax or dispense with it. If the Council refuses your application you could then appeal against this decision (in England) to the Department for Communities & Local Government, within one month of the refusal.