A review of current research shows insufficient monitoring and testing have been conducted to reliably assess the degree of environmental risks posed by transgenic crops. The major risks include increased resistance to particular pesticides, gene flow into related plant species, and negative effects on non-target organisms. Significant gaps in knowledge, often stemming from missing markets for ecological services, warrant a cautious environmental regulatory approach for transgenic crops. The objective of this paper is to identify the types of ecological systems public research to implement effective biosafety controls. US biosafety regulatory processes tend to focus on controlling type I error, i.e. restricting the release of the crops when significant environmental risks do not exist, because the economic losses from denying commercialization can be estimated. However, the precautionary principle, which focuses on controlling type II errors, i.e. releasing the crops when serious ecosystem damage will occur, adds a necessary criterion given the current deficit in ecological science. The key challenge facing regulators is to find the appropriate balance of controlling type I versus type II errors. The research program should embed the lessons of evolutionary biology and ecological sciences. Viewing the plant as a production machine that can be “brute-force” reengineered for more efficiency is a poor analogy. Unanticipated and unintended results, positive and negative, will emerge from such engineering because plants are complex systems embedded in poorly understood, complex, and interacting ecosystems. An ideal public research program should capture the interconnectedness of ecological systems, the essential roles of ecosystem services, nonlinear and threshold responses to accumulating stresses, and global expansion of the technology. Basic elements of such a program include long-term studies of cumulative and synergistic pesticide resistance effects, potential gene flow problems for those transgenic crop trait-weed complexes with high probabilities of outcrossing and ecological disruption, and scientific protocols for assessing deleterious effects on non-target organisms. For all three effects, expanded ecosystem monitoring of the commercialized crops in varied settings is needed for improved type II error definitions and estimates. The development of improved risk analysis methodologies and protocols should also be a priority. Finally, scientific effort to stimulate precautionary research, such as the development of transgenic crops that mimic ecological systems functioning, could avert many risks. Creating information to avoid significant ecological damages and foster precautionary research and development for transgenic crops are neglected roles of public biotechnology research.