In retrospective secondary data analysis studies, researchers often seek waiver of consent from institutional Review Boards (IRB) and minimize risk by utilizing complex software. Yet, little is known about the perspectives of IRB experts on these approaches. To facilitate effective communication about risk mitigation strategies using software, we conducted two studies with IRB experts to co-create appropriate language when describing a software to IRBs. We conducted structured focus groups with IRB experts to solicit ideas on questions regarding benefits, risks, and informational needs. Based on these results, we developed a template IRB application and template responses for a generic study using privacy-enhancing software. We then conducted a three-round Delphi study to refine the template IRB application and the template responses based on expert panel feedback. To facilitate participants' deliberation, we shared the revisions and a summary of participants' feedback during each Delphi round. 11 experts in two focus groups generated 13 ideas on risks, benefits, and informational needs. 17 experts participated in the Delphi study with 13 completing all rounds. Most agreed that privacy-enhancing software will minimize risk, but regardless all secondary data studies have an inherent risk of unexpected disclosures. The majority (84.6%) noted that subjects in retrospective secondary data studies experience no greater risks than the risks experienced in ordinary life in the modern digital society. Hence, all retrospective data-only studies with no contact with subjects would be minimal risk studies. First, we found fundamental disagreements in how some IRB experts view risks in secondary data research. Such disagreements are consequential because they can affect determination outcomes and might suggest IRBs at different institutions might come to different conclusions regarding similar study protocols. Second, the highest ranked risks and benefits of privacy-enhancing software in our study were societal rather than individual. The highest ranked benefits were facilitating more research and promoting responsible data governance practices. The highest ranked risks were risk of invalid results from systematic user error or erroneous algorithms. These societal considerations are typically more characteristic of public health ethics as opposed to the bioethical approach of research ethics, possibly reflecting the difficulty applying a bioethical approach (eg, informed consent) in secondary data studies. Finally, the development of privacy-enhancing technology for secondary data research depends on effective communication and collaboration between the privacy experts and technology developers. Privacy is a complex issue that requires a holistic approach that is best addressed through privacy-by-design principles. Privacy expert participation is important yet often neglected in this design process. This study suggests best practice strategies for engaging the privacy community through co-developing companion documents for software through participatory design to facilitate transparency and communication. In this case study, the final template IRB application and responses we released with the open-source software can be easily adapted by researchers to better communicate with their IRB when using the software. This can help increase responsible data governance practices when many software developers are not research ethics experts.