The head of an atheist group that has filed a lawsuit against prayer at Barack Obama's presidential inauguration says the government is picking a winner between "believers" and "those who don't believe" and subjecting atheists and agnostics to someone else's religious beliefs.

Dan Barker, co-president of the Freedom From Religion Foundation, has joined with Michael Newdow, who fought to have the words "under God" removed from the Pledge of Allegiance, in a federal lawsuit seeking to enjoin the Presidential Inaugural Committee from sponsoring prayers at the official inauguration. 

The 34-page legal complaint similarly seeks to enjoin Supreme Court Chief Justice John Roberts, Jr., from adding the phrase "So help me God" to the presidential oath of office.

"We're hoping to stop prayer and religious rituals at governmental functions, especially at the inauguration," Barker told FOX News Radio.

"The inauguration is not a religious event. It is a secular event of a secular country that includes all Americans, including those of us who are not Christians, including those of us who are not believers," he continued.

Barker, who said government's not picking sides on the issue of religion is "hard wired into our Constitution," called the 29 members of the suit all atheists and agnostics who love their country and participating in the inauguration. 

"Yet we are subjected to someone else's religious views with the endorsement of the government, which makes us feel like second class outsiders," he said.

The Freedom From Religion Foundation is the same group that fought to have atheist displays next to holiday displays, most notably in Washington state this year.

He said if Obama wants to hold a private religious ceremony, that would be more appropriate than having religious figures up on stage at his swearing in ceremony.

Peter Sprigg, vice president for policy at the Family Research Council, said it's Obama's decision whether to include a prayer, not the government's.

"The atheists, while they have every right to practice their atheism, they do not have an absolute right not to be exposed to viewpoints they don't agree with. So I think this lawsuit has no merit whatsoever," Sprigg said.

Barker argued that by allowing religious phrases to be used in the ceremony as well as inviting Revs. Rick Warren and Joe Lowery, who are named as defendants in the suit, to participate in the inaugural festivities, the government is picking a winner in the dispute over religion and atheism.

"Those people who do pray do believe in God and they are in fact trying to use the government to pick sides. In America we are free to disagree. We can disagree with Rev. Rick Warren but we're not free to ask our government to settle the argument," Barker said, adding that government causes harm when it takes on "the mantel of religion and expresses religion as an official governmental function."

Sprigg said he thinks the case has no merit and, like previous attempts to block inaugural prayer, this too will fail. 

"These atheists who are suing to prevent prayer at the inauguration are showing a fundamental misunderstanding of what the First Amendment is all about. The establishment of religion that is forbidden by the First Amendment means the official declaration of an official national church. It doesn't mean that public ceremonies can not include prayers or acknowledgement of the existence of God," he told FOX News Radio.

Asked if prayer is excluded, wouldn't that mean government is choosing atheists as the winner, Barker replied, "There is a difference between neutrality and hostility. 

"If the government were to invite me as a national atheist leader to get up and give an invocation that curses the name of God and that encourages people to stop believing and stop being so childish and divisive then that would be wrong because the government would be taking a pro-atheist position," he said.

Sprigg said he doubts that Roberts being named in the suit will affect the outcome or that Roberts would have to recuse himself if the case came before the high court .

"That's intriguing but I don't think even the liberals on the court would go so far as to prevent prayer at the inauguration," he said.