"I think we should put a halt on immigration, because our borders are broken, until we have a proper system to vet people. I think all immigration, but especially those coming from the Middle East right now," he said on "CNN Newsroom" with Carol Costello.
Starting on January 5 in Des Moines, Graham -- the son of evangelist Billy Graham -- will hold prayer rallies at all 50 state capitals.
"I'm asking for Christians to join me -- or anybody -- to join me at the capital and to pray for our nation," he told Costello, adding later, "Everybody's welcome. Absolutely. Muslims will be welcomed."
Graham, who is president and CEO of the Billy Graham Evangelistic Association, has long been a vocal advocate for socially conservative issues, including moving his organization's accounts with Wells Fargo away from the bank after it showed an ad featuring a lesbian couple
. Graham was also criticized in 2012 for refusing to say that President Barack Obama was Christian
Graham heads Samaritan's Purse, a humanitarian organization that provides aid to Middle Eastern refugees.
Graham told Costello he "loves Muslims" and "works with Muslims," but after Donald Trump proposed a temporary ban on Muslim immigrants following the San Bernardino shooting, Graham agreed with the Republican front-runner.
"For some time I have been saying that Muslim immigration into the United States should be stopped until we can properly vet them or until the war with Islam is over. Donald J. Trump has been criticized by some for saying something similar," Graham posted on Facebook.
Graham also said Islam is not compatible with American values and therefore the U.S. might have to shut down mosques.
"We might have to at some point. I don't know," he said. "We have a responsibility -- our government, the President, our Congress -- has a responsibility to protect all Americans."
Graham said he will not endorse anyone this election but is encouraging Christians to vote for candidates that support "biblical principles, godly principles, because those principles work."
"We need more Christians in politics. I want to encourage Christians to run for every political level," he said. "I'm not talking about just at the presidential level, I'm talking about all levels of government."
"Our nation is crumbling. We're in turmoil. Washington does not work. We need to get people in office who are willing to work with one another and who uphold Biblical principles," he added.