Welcome to the forum and congratulations on owning a PT99 (I own two and love them).
First of all, try shooting it from a solid bench rest or sand bags and see how it does. If you still have the problem, check that rear sight for anything like the elevation screw being loose (or worse, missing).
I had problems with my PT709 shooting low and left, and everyone was telling me it was the way I held it, or the way I squeezed the trigger, or that I was flinching, yadda, yadda, yadda. All good sound advice but it was funny that I'd been shooting well over 55 years and it was the only pistol I own that consistently shot low and left and it didn't matter if I used a bench rest at 10 feet, it was still shot low and left.
I eventually had to shim up the rear sight and modify the mounting holes to and move it as far to the right as the adjustment would allow to get it on target. I have several PT92/99/ a PT100, and a PT 917, and they all shoot pretty close out to 25 yards, but the 709 was a problem. Luckily, if I ever have to use it, the sights won't come into play because it will be at "point & shoot" range.