I own a Punto ELX W reg and I have a similar noise coming from the rear suspension. I did quite a bit of reading on this and had the car checked at a garage and they suggested that because both of the rear shock absorbers have developed slight rust on the inner tube, this is rubbing against the outer tube, thus creating this kind of clonking/rattling noise.
Apparently, the rattling noise (not the rust) is a common design fault on all MKII Puntos and whoever discovered this quickly enough had the whole rear subframe replaced by FIAT under warranty, provided the car was under 3 yrs old, of course.
The garage told me that it is perfectly safe to drive the car if I could live with the noise. It does get a bit irritating sometimes, however, I've lived with it for more than two years now. Because your Punto makes the noise from only one side, I suggest you make sure that it doesn't come from the other side, too and if not, then get your shock absorbers and rear suspension bushes checked for their condition. If it is the bushes, this is usually a quite inexpensive job. However, expect to pay a lot more for new absorber(s).
Good luck!