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The solution depends on many factors. First, it is important that you are performing the tests following FS209E or ISO 14644 standards. I recommend that you consult these standards to be certain of your measurement. Second, the greatest source of particles is people. Again, you should refer to the standards as they specify the test methods concerning the presence of people. To get the best results consider leaving the cleanroom closed for 24 hrs before taking samples. Also, I would consider increasing the sample time as the counts will be high initially because of the human contact. Leave the particle counter running for 24 hrs if possible.
If you continue to see high counts then you need to consider replacing your air filters.
Go here to learn more about monitoring cleanrooms.
For a more thorough understanding of particle counting read The Basic Guide to Particle Counting.