Violence outside a Coptic Christian cathedral last weekend left five Christians and one Muslim dead. Conflict erupted following a funeral service for Christians killed during earlier melees.
Deputy Director for Middle East and North African at Human Rights Watch Nadim Houry called on Morsi to take a close look at the festering violence between the religious communities.
The rights group said violence between Muslims and Christians in Egypt has escalated since 2008, three years before the country's revolution. Since Morsi came to power in June, however, there's been no serious investigation into the sectarian violence.
Nearly two dozen members of the Coptic community were killed in an attack on a church in Alexandria in January 2011.
Morsi's administration has been criticized for appearing to favor Islamic ideologies. He hails from the Freedom and Justice Party, the political arm of the Muslim Brotherhood.
There's been no indication that his policies were related to the latest violence. Existing laws discriminate against Christians, however.
"President Mohamed Morsi needs to acknowledge the deep and longstanding problem of sectarian violence in Egypt and take decisive steps to address it before it escalates further," Houry said in a statement from New York.