The Women, Peace & Security program was signed into law by Trump and had received backing from numerous Republican leaders.
The Defense Inspector General's Office will look into whether the defense secretary improperly shared sensitive information on the commercial app.
Republican and Democratic leaders on the Senate Armed Services Committee are requesting a formal investigation into the Signal chat scandal.
Former U.S. defense officials said the unsecured messaging chain could have jeopardized the operation and put American lives at risk.
