Non-governmental organizations are taking an increasing role in creating incentives for private landowners to protect endangered species habitat. In some cases, private organizations have administered government-funded programs, such as the roles of The Peregrine Fund and The Nature Conservancy in administering safe habor programs in Texas and Virginia, respectively. Ducks Unlimited provides the technical expertise behind Hawaii's endangered waterfowl Safe Harbor agreement.

Now two private organizations have created their own incentive-based programs to help landowners help endangered species. The North Carolina Herpetological Society is paying landowners who are willing to protect the habitat of imperiled bog turtles that reside on their land. In the Hill Country of Texas, Environmental Defense has created the Landowner Conservation Assistance Program, which is funding ranchers who undertake management activities that benefit two endangered songbirds, the golden-cheeked warbler and the black-capped vireo. In December 2000, Environmental Defense initiated a safe harbor agreement for landowners restoring habitat for these birds.