Shafiq and Alaa and Gamal Mubarak were accused of misappropriating funds in the Pilots' Association for Land Development in the 1990s, with Shafiq accused of seizing land belonging to fishing farms and allocating it to the association then selling the land to Mubarak's sons at below-market prices.
Also acquitted were former Air Force Gens. Nabil Shoukry and Mohamed Reda, both former association officials who were defendants with the Mubaraks and Shafiq, Ahram Online reported.
Shafiq, who was tried in absentia, lives in Dubai where he fled after losing the presidential election runoff to the Muslim Brotherhood's Mohamed Morsi in 2012. Morsi was ousted this summer by the military.
A verdict in a separate corruption trial against Shafiq was expected to be announced soon.
Alaa and Gamal Mubarak also face separate trials on other corruption-related charges.