The arrival of Islamic State provided only the "tipping point" in a wider trend of believers leaving the countries, according to the document, which also warned that providing precise figures was difficult.
The report comes as United States-backed Kurdish-led forces began an operation to seize control of the Syrian city of Raqqa.
It also estimates that the Christian community in Iraq has shrunk from more than 300,000 in 2014 to 200,000-250,000 today - "many" of whom are internally displaced.
Concerning Syria, the 'Understanding the recent movements of Christians leaving Syria and Iraq' report estimates that the Christian population of around two million six years ago has "roughly halved".
The document - compiled by three Christian charities; Open Doors, Served and Middle East Concern - warns Syrian and Iraqi Christians are experiencing "overall loss of hope for a safe and secure future".
It also warned that many believers who have left Syria and Iraq see "little incentive" to return. Several interviewees were quoted as saying "the Middle East is no longer a home for Christians".
The report lists conflict, violence, the near-destruction of historically Christian towns in the Nineveh Plains of Northern Iraq, other people emigrating, loss of community, higher prices, and a lack of job and education opportunities as driving factors in the exodus.
Thousands of Christians have been accepted into Lebanon, Jordan and Turkey. A smaller number arrived in European countries such as Sweden and Germany; the report warns some are facing an "incredibly difficult" experience in Europe.
The three organisations call upon the European Union to help make sure those responsible for religious or ethnic persecution and discrimination in Iraq and Syria are held to account.
The report also concluded "many" of the Christians who remain "want to play their part in rebuilding the shattered societies of Iraq and Syria."