His remarks came during a speech at Egypt's Al-Azhar, the Sunni Muslim world's foremost religious institution, where he met Grand Imam Ahmed al-Tayeb.
"Around the world, we are seeing ever-rising anti-Muslim hatred, anti-Semitism, racism and xenophobia," the UN secretary general said.
He cited the 15 March New Zealand mosque attacks by a white supremacist as well as a 2018 synagogue shooting in Pittsburgh that killed 11 people and is believed to be the deadliest against Jews in US history.
Guterres warned of a surge in hate speech he said was "entering the mainstream, spreading like wildfire through social media".
"We see it spreading in liberal democracies and as well as in authoritarian states."
Guterres is on a two-day trip to Egypt, following his visit to Al-Azhar, he was scheduled to meet President Abdel Fattah al-Sisi.
On Sunday, he attended an Arab League summit in Tunisia.