The federation said in a statement issued Monday night that it will evaluate whether Herrera, striker Oribe Peralta and midfielder Marco Fabian violated its code of ethics, which calls for "maintaining a neutral position on matters of a religious or political nature."
Local media reported that they face possible fines.
Herrera, affectionately known by his nickname, "the Louse," is famous for his exuberant sideline displays during last year's World Cup in Brazil.
But he drew a backlash for tweets backing the Green Party, which ran a slick advertising blitz and was fined millions of dollars for violating campaign laws.
"Don't forget to vote, let's go with the Greens," and "The Greens fulfil" their promises, Herrera said Sunday on Twitter. Green is traditionally the Mexican national team's colour, but the "The Greens Fulfill" was a party campaign slogan.
Electoral law forbids campaigning by parties on election day, but Green Party officials said they had nothing to do with Herrera's tweets or a series of very similar messages sent by a variety of television and music stars.
Herrera was defensive about the tweets at a news conference Sunday, after the national team lost 2-0 in a friendly match with Brazil.
"I'm a human being, I'm a normal Mexican citizen, with statements that I can make in social media," Herrera said. "It's simply a personal situation."
Peralta, who plays professionally for Club America of Mexico City, sent tweets urging Mexicans to vote using a hash tag that translates as "WearGreen" and was used by others to promote the party. "I want a #GreenMexico!" he tweeted Sunday.
Fabian, of Guadalajara's Chivas, retweeted Herrera and also posted one of his own using the "WearGreen" tag.