Totally agree with the others.
What kind of foodstuff is being analysed?
Is it shelf stable or chilled?
What size of sub-sample are you taking for analysis and what are you sending of?
What types of tests are being carried out? Assumably indicator organisms?
Again, what methods?
An example is E. coli - many labs use pour/spread plate on TBX agar then incubate at 44 degees C for 24 hrs. Many other labs incubate at 37 degrees for 4 hours first to minimise stressed cells , then transfer to 44 degrees C.
However, another very common method is the membrane method, which in my experience is a much more sensitive test and I always get higher recovery when analysing the same inital suspension using both methods.
Anyway, just to give you a few examples...
Assumable you are analysing prior to the extrnal lab. If microorganisms are present beforehand and obviously depending on conditions, they may have scope to grow, therefore giving a higher result later.
Give us more information.