The Federal Aviation Administration has launched an investigation into allegations that New York and Texas airports discriminated against Chick-fil-A by barring the fast-food chain over the owner’s stance on LGBT issues.

According to the FAA, the US Department of Transportation “received complaints alleging discrimination by two airport operators against a private company due to the expression of the owner’s religious beliefs.”

San Antonio International Airport and Buffalo Niagara International Airport have been informed by the FAA’s Office of Civil Rights that it has opened investigations into those complaints.

“The FAA notes that Federal requirements prohibit airport operators from excluding persons on the basis of religious creed from participating in airport activities that receive or benefit from FAA grant funding,” the FAA said in a statement.

“The findings of the investigations will be communicated to the complainants once the investigations are completed.”

Chick-fil-A, an Atlanta-based chicken sandwich chain, has come under fire in years past for donating millions to groups that oppose same-sex marriage.

Dan Cathy, the chain’s CEO and a known critic of gay marriage, said in 2012 that the restaurant chain supported “the biblical definition of the family unit” and that marriage equality was “inviting God’s judgment” on the US.

Chick-fil-A said in a statement to The Post on Wednesday that the chain “did not initiate, nor are we involved in this investigation.”

“We are a restaurant company focused on food and hospitality for all. We are grateful for all our customers and are glad to serve them at any time.”

With Post wires