The actions were the same, but the Type 99 had a shorter barrel than the Type 38. Type 99's also had fold out anti aircraft sights. Early 99's had a sheet metal sliding dust cover over the action (usually discarded by troops in the field) and a fold down monopod under the forearm.
Basically the same but with the changes I enumerated above.
Type 38's were also issued with dust covers as well as 99's.
Not all 99's have anti aircraft sights either.