The agency initially approved giant reed and napier grass for the program last January, before withdrawing it two months later once environmental groups grew concerned. The groups warned that encouraging growth of the two plant species could push native plants out of some regions.
Last year, organizations including the Natural Resources Defense Council and the National Wildlife Federation sent a letter to the agency worrying that the rule would be "likely to lead to the spread of invasive species without any kind of analysis on the potential harm caused by the promotion of the invasive species or determination of the benefits."
They claimed that approving the species would be a violation of a 1999 executive order prohibiting a federal agency from activities that "it believes are likely to cause or promote the introduction or spread of invasive species in the United States or elsewhere" unless the benefits outweigh the potential harm.
Neither giant reed nor napier grass are native to the United States.
In its rule, the EPA admits that the crops act like invasive species. The rule includes additional requirements on registration, reporting and record keeping for the plants.
"These additional requirements are necessary to minimize the potential that the feedstock will spread to areas outside the intended planting area," the agency said in its rule.
The final rule was signed by acting EPA Administrator Bob Perciasepe on Friday.