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(CNN) Pope Francis reaffirmed his disagreement with teaching gender identity in schools on Sunday, after earlier calling it a "war against marriage."

On a return flight to Rome at the end of a three-day trip to Georgia and Azerbaijan, the Pope recounted a meeting with a French father whose young son wanted to be a girl after reading about it in a textbook.

"This is against nature," he said. "It is one thing when someone has this tendency ... and it is another matter to teach this in school."

"To change the mentality — I call this ideological colonization," the Pope said.

The Pope said he still spends time with transgender people, leading them closer to God.

In August, the Pope called the teaching of gender identity theory "terrible."

Related: Pope: Gays and Others Marginalized Deserve an Apology

"Today, in schools they are teaching this to children -- to children! -- that everyone can choose their gender," Pope Francis said.

New Ways Ministry, a Catholic LGBT advocacy group, criticized those remarks.

"The pontiff's remarks are further evidence that church officials need desperately to educate themselves about the lives and experiences of LGBT people," said Francis DeBernardo, executive director of New Ways Ministry.

"Nobody chooses a gender identity. They discover it."

As a new Pope in 2013, Francis made headlines around the world for his progressive stance on homosexuality.

"If someone is gay and he searches for the Lord and has good will, who am I to judge?" Francis asked.

The position appeared to be a shift from the traditional Catholic stance on homosexuality as a sin.