There is no one-size fits all to handling customer due diligence and enhanced due diligence. When looking at your NGO's, you should consider the source, type and frequency of their deposits. At account opening, ask what their anticipated activity will be. Monitor to see if there are unusual spikes in activity that you cannot explain. (A spike in deposits by a church at Christmas and Easter can probably be explained by an increase in attendance. A spike in deposits during Girl Scout Cookie season is also easily explainable.) Many NGO's will accept donations or annual dues in cash so this is not uncommon.
You should also ask and monitor to see where the funds are going. If the stated purposed of an NGO is raise money for a sick child, but you start seeing the account signers initiate several wire transfers that are not going to a doctor or hospital, you can start to see some red flags.
Just because an account relationship is in a higher risk class does not automatically make the account high risk. As with due diligence on any account, you have to ask, "How well do I understand the organization and its purpose? and "Does the activity seem justified based on my knowledge of the organization?"
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