It is a program that was started back in the 20s or 30s to stop the spread of some major chicken diseases. When they tested mine they checked mainly for puloram and avian flu. You have to be NPIP certified to ship live poultry legally.
I called my local ag department who gave me the phone number of the state vet (who knew we had one of those?) and the vet gave me the number of the local tester.
I called the tester and he came out one afternoon and drew blood from a sampling of my chickens and sent it off to the state lab. The lab sent back a letter with the scores and a card with my NPIP number on it. I called the tester and he sent me a packet of info and a stack of forms to include when I ship birds. I paid the state $25 for the year. You have to be certified once a year.
The hardest part was catching the darn chickens to test them.
The NPIP program is strictly voluntary, but different states have different restrictions and requirements regarding poultry. Be sure to check your state to find the specific requirements. For example, I live in Virginia. I can ship live poultry inside the state of VA and I do not have to be NPIP certified. I can also ship live poultry to any other state in the US without being NPIP certified UNLESS the state I am shipping to requires me to be NPIP certified. However, any poultry being shipped into VA from another state must be NPIP certified. Also, say I want to go to a show, a swap, etc. in another state, some of those states require NPIP certification. It is very simple and relatively inexpensive to become NPIP certified. I don't have to pay the state for certification, but I do have to pay the fee the tester charges.
Here is a link to the APHIS website regarding NPIP. Hope that helps.
Just to clarify, NPIP was started in order to protect the food supply, not to certify backyard flocks as healthy, which it does not. It does not test for the most common poultry diseases like mycoplasmosis unless you pay extra and test much more often than once a year. Not even hatcheries are usually certified MG free. So, just don't make it something that it isn't. I see all the time that it's mentioned here on BYC as meaning someone's flock is completely healthy if they are NPIP and nothing could be further from the truth. It is usually required for mailing hatching eggs and/or live birds into another state, plus some states want an additional permit as well.
I broke down and got certified purely so I could ship adult birds. All it does is provide paperwork that says I am pullorum free and avian flu free. It does not cover the myriad of other possible illnesses.