Surely NASA has the ability to fashion nooks and crannies that escape routine public disclosure requirements. For example, NASA might do a joint project with the DARPA, with the project governed by military secrecy until NASA and DARPA agree to issue a public report.
They have the ability but I don’t think they are doing secret programs. They aren’t set up for that, and they kinda suck at keeping secrets.
DIA, DARPA, those kinds of entities would be able to (and have done so).
https://www.amazon.com/Intercept-UFO-Renato-Vesco/dp/B0006WI572