I've seen this same situation about 100 times as an engineer. If you use the % sign, then 0.3% is correct. If you specify 0.003, you might want to put a comment to the side saying either "0.03 = 3.0%" or "0.01 X %". It is important that all parties using the number understand what units they are dealing with.
To answer you simply, either is correct, so long as the units are clear to everyone.