There is no USDA tolerance level for GMOs in organic food. The use of GM seed is an “excluded” method. The organic program is “process-based” and therefore no threshold levels are established.
Here is a great fact sheet from USDA-AMS on this topic: http://www.ams.usda.gov/AMSv1.0/getfile?dDocName=STELPRDC5090396.
Here is an excerpt from that fact sheet:
Has a tolerance level (e.g. 5%) been established for the presence of GMOs in organic agricultural products?
The NOP regulations do not establish GMO tolerance levels. The NOP regulations establish a tolerance for the presence of pesticides registered by the U.S. Environmental Protection Agency (EPA) that is set at 5% of the EPA tolerance level for the specific residue detected. No federal agency, including EPA or USDA has established tolerance levels for the inadvertent presence of the products of excluded methods (GMOs).
Certified organic food cannot contain GMO ingredients. The use of genetic engineering is one of the "excluded methods" described in the Terms Defined section of the National Organic Program Regulation, available here.