This is a partial transcript from "The O'Reilly Factor," September 27, 2005, that has been edited for clarity.

Watch "The O'Reilly Factor" weeknights at 8 p.m. and 11 p.m. ET and listen to the "Radio Factor!"

BILL O'REILLY, HOST: Tonight it's estimated more than a half million hurricane evacuees were given help by religious groups inside the hurricane zone. Now the federal government says it will reimburse some of those churches and facilities for providing food, shelter and other support.

But not so fast. A variety of so-called civil liberties groups are objecting to the federal reimbursement.

Joining us now from Washington is Reverend Barry Lynn, the executive director of Americans United for Separation of Church and State (search).

Think this is just another attack on religion? FEMA (search) says that we'll reimburse, and I'm quoting now, "reimburse religious organizations that have operated emergency shelters, food distribution, medical facilities at the requests — at the request— of state or local governments in three states that have declared emergency, Louisiana, Mississippi and Alabama."

So Reverend, you're going to tell me that the state comes in to St. Bridget outside of New Orleans (search) and says, gee, to the pastor, would you feed evacuees and shelter them in your gymnasium, and of course the pastor is going to say yes. And then St. Bridget is not entitled to be reimbursed?

REVEREND BARRY LYNN, AMERICANS UNITED FOR SEPARATION OF CHURCH AND STATE: Well, I'll tell you. This is not an attack on religion, but it is an attack on FEMA. Here's an organization that did a dismal job at disaster relief to begin with.

Now what they're trying to do is do an equally dismal job of trying to defend the religious rights of all the people in these affected areas. For example, if you read these FEMA guidelines, I think you would be shocked. There is nothing in them that calls for any kind of level of accountability to the American taxpayer for where this money is going, what it's being used for.

O'REILLY: OK, but...

LYNN: And also no protections against discrimination

O'REILLY: Religious groups like secular non-profits will have to document their costs, file for reimbursement and provide paperwork for FEMA. But let's get back to real life. I don't want to go into theoretical. It's boring and we don't do that here. St. Bridget was asked by the state of Louisiana to feed and shelter evacuees. St. Bridget did that. Now St. Bridget — I'm making that up. It could be St. (INAUDIBLE), it could be some Protestant church or it could be a temple. All right? They do it. You're telling me they are not entitled to government funds reimbursing them?

LYNN: No, what I'm telling you is that under the FEMA regulations, they may well not be entitled to this because the FEMA regulations don't tell us what we need to know. What we need to know is does that church, for example — your hypothetical church — is it willing to allow everybody who needs help to come into that church?

And here's another — this is very practical because we're representing some people outside of the context of the hurricane in this disposition. Let's say there's a guy named Bill O'Reilly (search) who goes down to a Protestant church in New Orleans and says, look, I want to be a volunteer to do hurricane relief. And the guy at the door says, O'Reilly, you know that sounds like maybe an Irish-Catholic name. We don't really — we can't use Catholic volunteers because this is a Protestant church. Now under the FEMA administration and George Bush (search) administration, they think it's perfectly permissible for that discriminatory operation to be able to get reimbursed with tax dollars.

O'REILLY: How do we get...

LYNN: I say that's bunk. I say that's baloney and if they're not going to defend the legitimate rights even of volunteers, they don't deserve...

(CROSSTALK)

O'REILLY: You're into the theoretical again. They asked...

LYNN: It's not theoretical. This is practical. This is happening.

O'REILLY: They asked certain — yes, but not in the hurricane zone. It's not happening there and if it is, you need to provide documentation for it, and you can't right now. If it is, I might take a look at it. Right now, you're objecting and the other civil liberties, which is just the biggest misnomer in the world, are objecting in theory to helping churches who have helped the evacuees at the behest of the state and it's wrong. It's wrong. It's morally wrong.

LYNN: No, Bill.

O'REILLY: It's wrong in every single way.

LYNN: Here is what's wrong. Most of those churches, by the way, are not seeking one dime of compensation.

O'REILLY: It doesn't matter if they're seeking it or not.

LYNN: Wait a minute. Wait a minute. They are doing charity work. They are doing work out of the spirit that brings them to their religious faith in the first place. They are not coming back to Washington, secretly or otherwise, and asking the government to compensate them in an unheard of, unparalleled effort for the good work that they have been doing.

Furthermore, you cannot give money — just throw it into the collection plate from the taxpayers' pocket without asking the right questions. Are you discriminating against the people that you're trying to serve?

O'REILLY: If you can.

(CROSSTALK)

O'REILLY: I would consider that discriminatory.

LYNN: All right.

O'REILLY: But right now, you are blanketly objecting to reimburse these people who deserve to be reimbursed, even if they don't ask for it, Reverend. They did good work. It's another attack on religion. And it's wrong.

LYNN: It's not.

O'REILLY: You get the last words.

LYNN: It is an attack on FEMA and it is an attack on the idea that you just give money to religious organizations without asking them to play by the same rules that secular groups do, and act in a non-discriminatory fashion, and don't try to convert people to their viewpoint. That's called fundamental fairness. There's nothing wrong with asking for that.

O'REILLY: All right, Reverend, thanks very much.

Content and Programming Copyright 2005 Fox News Network, L.L.C. ALL RIGHTS RESERVED. Transcription Copyright 2005 eMediaMillWorks, Inc. (f/k/a Federal Document Clearing House, Inc.), which takes sole responsibility for the accuracy of the transcription. ALL RIGHTS RESERVED. No license is granted to the user of this material except for the user's personal or internal use and, in such case, only one copy may be printed, nor shall user use any material for commercial purposes or in any fashion that may infringe upon Fox News Network, L.L.C.'s and eMediaMillWorks, Inc.'s copyrights or other proprietary rights or interests in the material. This is not a legal transcript for purposes of litigation.