In a PE/N supply will I have a large difference or by connecting two different groups of earth pits together while the distance between the two is about 60meters apart from each other ?
Possibly (but it depends on the sort of analog equipment, isolation devices and interconnection and interaction between them).
A good (compliant to local regulations) safety earth does not necessarily mean a good analog signal earth. If you are having issues with signal noise (which you mention you are having) then consider connecting your signal earths to a single (star) point to minimise earth loops, or possibly a separate isolated analog earth connected to the main safety earth at a single point.
Hopefully this general information helps. Also see the numerous previous threads on CR4 on earthing and grounding for more information.
Can you provide more detailed information on your site, its wiring setup and its problems?