The group said it had documented attacks on 42 churches and dozens of Christian institutions, schools and homes, as well as Christian-owned businesses across the country.
It said at least four people were reported killed in sectarian violence, three Christians and one Muslim.
Attacks on Egypt’s Christian minority have escalated since the July 3 ouster of Islamist president Mohamed Morsi.
The attacks dramatically increased since the August 14 dispersal of two pro-Morsi protest camps in the capital.
Human Rights Watch said authorities had failed to protect Christians from attacks, and that Islamists, including Morsi’s Muslim Brotherhood, had failed to properly condemn the violence and prevent future attacks.
“For weeks, everyone could see these attacks were coming, with Muslim Brotherhood members accusing Coptic Christians of a role in Mohamed Morsi’s ouster, but the authorities did little or nothing to prevent them,” said Joe Stork, the group’s acting Middle East director.
“In the vast majority of the 42 cases Human Rights Watch documented, neither the police nor the military were present at the start or during the attack,” the group said.
It said a priest in Minya province told the group he had called police and emergency services multiple times as mobs attacked his church, but no one came.