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By how much is the file size increasing? Depending on how you do the actual encryption, it can easily grow a bit due to varying headers and some padding, but it shouldn't be a significant part of the file size if the file is reasonably big.
If, however, the file size grows by some significant factor (say your output is 2 time the size of the input), then there is some problem that you should look into.
I suspect that this is a cross post of [http://www.coderanch.com/t/499442/java/java/RAS-public-private-key-encrypt|http://www.coderanch.com/t/499442/java/java/RAS-public-private-key-encrypt].