The study by Christian Solidarity Worldwide documented that since 2011 there has been a rise in the number of blasphemy cases brought against Christians and that perpetrators of attacks against religious minorities generally enjoy impunity.
The report also found there are still serious restrictions on church-building in the country.
The publication of the report coincides with the second anniversary of the beheading of 21 Coptic Christians on an Egyptian beach in an Islamic State video.
The charity's Egypt Advocacy Officer - who can't be named for security reasons - told Premier News Hour that they are working with the Egyptian government to help improve the situation for Christians.
"There will be an attack on a community, the security services may know about it before hand and do nothing, there's precious little follow up for the Christian community in terms of justice."
He added: "We're making recommendations to try and encourage the Egyptian government in everything they've done well but also pointing out to everyone here that there are serious areas of concern where we want to see the Egyptian government do better."
Egypt's Coptic Christian community is still recovering after Islamic State suicide bombers murdered 27 believers at St George's Orthodox Cathedral in Cairo in December.
The country is number 21 on the Open Doors' World Watch List of the 50 most difficult countries in the world to be a Christian.