I would understand the sentence to mean that someone is alleging that there has been a fraud committed against the government, that is, they are claiming that the government is the victim of a fraud.
Depending on context, one could understand these words to mean that they are making an allegation against the government, and that the allegation is that there is fraud.
That is, you could group the words as "(alleging) (fraud against the government)" or "(alleging fraud) (against the government)".
There is some ambiguity because the preposition "against" could go with "allegation" or with "fraud". That is, we could read it as there has been fraud against the government, or that someone is bringing an allegation against the government.
But the first reading is more likely, and the fact that it says "for the government's benefit" would support that. If the government is the victim of fraud, then bringing it to light would be for the government's benefit. If the government had committed fraud, then bringing it to light would be for the benefit of the person the government had defrauded.
To be sure you'd have to read the larger context.