This kind of sentence is called a "passive" sentence. You use "have been ___ed" when you don't want to say who did something because you're trying to hide it, or just because it's not important.

If someone asks about the dishes in the dishwasher:

Have these been run?

...the speaker asks "Have these been run" instead of "Did you run these?" because it's not important who ran the dishes. It could be any member of the family.

In the example:

Yes, I just wanted to verify that my payment has been received?

...the speaker doesn't know exactly who receives the payments. All that's important is that the correct person or department received it.