That is only a national problem if the NGO's are getting their money from the government.
If the NGO's are private organizations getting their money from private citizens who donate voluntarily, then their fraud is less harmful, because I am not being required to contribute to their fraud. When I donate to a charity, I check to see what their overhead is, to assess the risk of fraud. If 60% of it is going to the executives to attend conferences in Switzerland, or the like, I know that their public assistance spending is merely a cover for their fraud, so I don't donate. However, if the money is coming from the government, the government doesn't stop donating. Indeed, the NGO just lobbies harder, and promises kick backs, jobs, and speaking opportunities to make sure the government money flows no matter what.
All the liberals who are funding the KKK and other racists groups by way of donating to the Southern Poverty Law Center ... it would be worse if the government were giving money to the SPLC. If the government gives money to the KKK by using the SPLC to hide the transfer, we have institutional racism and institutional fraud; but, if Democrat voters give money to the KKK as a result of SPLC fraud, we don't have an institutional problem.
Private charities, in general (not all the time, but more of the time), take care of their money better than the government does.