The comment, seemingly meant as a dig at the president's "Make America Great Again" slogan, drew laughter and gasps from the crowd on Wednesday and swift backlash on social media.
Cuomo at the event, which included a bill signing for an anti-human trafficking measure, went on to say that America "...will reach greatness when discrimination and stereotyping against women, 51 percent of our population, is gone. And every woman's full potential is realized and unleashed and every woman is making her full contribution."
Trump responded on Wednesday night, tweeting that Cuomo was having a "total meltdown."
In a statement sent several hours after Cuomo's comments, his press secretary Dani Lever sought to clarify the governor's comments.
"Governor Cuomo disagrees with the President," Lever said in a statement sent to ABC News. "The Governor believes America is great and that her full greatness will be fully realized when every man, woman, and child has full equality. America has not yet reached its maximum potential."
Lever also referenced how some associate the president's slogan, "Make America Great Again", with the history of sexism and racism in this country.
"When the President speaks about making America great again - going back in time - he ignores the pain so many endured and that we suffered from slavery, discrimination, segregation, sexism and marginalized women's contributions," the statement read.
Cuomo's primary challenger, actress and activist Cynthia Nixon did not respond to ABC News' request for comment.
Republican gubernatorial candidate Marc Molinaro tweeted a statement calling for an apology and said the governor "should be ashamed of himself."
Trump's former press secretary Sean Spicer has also taken to Twitter to respond to Cuomo's comments, mentioning the governor's "change" in tone.