The answer is no.
Here is what the Green Roof and Solar Department at the NYC DOB told me:
The building code does not explicitly provide a threshold for when a green roof installation would require a permit. The department is currently developing rules to provide guidance. In the meantime, a green roof installation is regulated in a similar manner to a roof replacement.
Under current department rules, a replacement in kind of roofing membrane does not require a permit; however, any roof replacement must still abide by the code. For example, the added thickness of a membrane cannot reduce the height of the parapet wall below that required by the code.
Furthermore, any roof replacement that increases the load on the roof structure beyond its bearing capacity, then additional work must be performed to increase the bearing capacity of the roof which also requires a permit. If the scope of the roof replacement alters the roof deck, then a permit must be obtained.
With respect to green roofs, many green roof systems add significant loads to the roof structure by way of the plant materials, growth medium, containment, and water. I highly recommend that you retain the services of a New York State registered architect or professional engineer to evaluate your roof prior to any green roof installation in order to verify the load bearing capacity of the roof.
If the green roof installation will require alteration to the roof deck or roof structure, then you must obtain a permit. Many green roof systems do not require deep growth media and as such do not pose a significant addition to the dead load of a roof.
As a general guideline, the department will not require a permit for green roof installations where the depth of the growth medium and containment does not exceed 4 inches in depth. However, again we would stress that you retain the services of an architect or professional engineer to evaluate the particular conditions of your roof, and any roof installation must still abide by the building code.
Furthermore, the New York City Fire Code requires Fire Department access to flat roofs of buildings that are 100 feet or less in height. Please refer to the Fire Code section 504.4 for more details.
If you fail to provide the Fire Department access, you may be found in violation and subject to penalties by FDNY.
Eco Brooklyn is a New York and Brooklyn green roof installer so this information is very important to us. If a client wants to take advantage of the $4.50/sq.ft. tax rebate then they do need to file for a permit. Sometimes if there is also a deck on the roof that is taking up space then given the small size of brownstone roofs it does not pay to go through the added work and expense of filing.
If you only have a 200 sq.ft green roof it is not worth paying $2,000 to file the job when you only get $900 in tax rebates. And yes filing a green roof job is expensive compared to other jobs of the same size because the paperwork is so tedious and the DOB is so reluctant to file it (though not understanding it and fear they are doing something wrong).