Yes. According to a NASA study [1], Falcon 9 development would cost $1.3B as Cost Plus Fee ("traditional NASA") or $443M Firm Fixed Price ("more commercial approach"). Compare to SpaceX actual of "about $300M".
[1] http://www.nasa.gov/pdf/586023main_8-3-11_NAFCOM.pdf
Edit: NASA originally came up with the $4B/$1.7B estimates that InclinedPlane mentioned. They visited SpaceX, saw how they actually operated, and revised the estimated downward.