Perry participated in a prayer at a student assembly last week at an East Texas middle school, ignoring the 1963 U.S. Supreme Court ban of organized prayer in public schools.
"Any time you have a crisis that faces you either in your personal life or as we have now in our country, reaching out to a supreme being is a very normal act," he said Monday in a news conference.
"Why can't we say a prayer at a football game or a patriotic event like we held at Palestine Middle School? I don't understand the logic of that. I happen to think it was appropriate."
Perry, a Republican, told reporters he would stand by his actions and he would make school prayer an issue in his election campaign. The former lieutenant governor succeeded Gov. George W. Bush when he was elected president.
Perry took part in a prayer offered by a Baptist minister last Thursday at the school in Palestine, a town about 90 miles southeast of Dallas.
School prayer has always been a hot issue in Texas and the Supreme Court ruled in a case last year that organized prayers before high school football games were unconstitutional.
Several civil rights groups have spoken out against Perry's position on the issue.
The Texas Freedom Network will ask it's more than 9,000-member families to write Perry and ask him to rethink his position, according to Samantha Smoot, the group's executive director.
"Religious freedom is a patriotic human value but religious coercion is not. While we agree with the governor that this is for many people an important time to pray, it is never a good time to have state-sponsored prayer in our schools," she said in an interview Tuesday.
Smoot said it is unclear to her whether Perry understands the law on school prayer.
"So either he is confused about the law or he's taking advantage of a time of national upheaval and insecurity to push an agenda," she said.
Smoot said the mission of the freedom network is to "advance a mainstream agenda of religious freedom and individual liberty to counter the radical right." It was formed in 1995 in Texas to monitor local school boards and the State Board of Education.