Catholic bishop of Hyderabad, Bishop Samson Shukardin, said other faith minorities were using different names too, to prevent them from being subjected to abuse.
He told Catholic charity Aid to the Church in Need: "Many minorities give their children Islamic names so they will not be singled out as Christians and become potential targets for discrimination.
"In many cases, minority students do suffer abuse in public schools."
Bishop Shukardin explained that the textbooks in state-run schools were a problem, saying: "The minorities are considered infidels and they are depicted negatively in textbooks, which promote prejudices against minorities.
"The fundamentalists believe that Islam is the only complete religion - that salvation is only found in the Qur'an as the last holy book."
Kidnappings and forced marriages are also common in rural areas where people have little education.
Archbishop Sebastian Shaw of Lahore archdiocese and Bishop Shukardin stressed the importance of education to limit kidnappings and to provide Church-run schools and colleges in Pakistan.
Bishop Shukardin said: "We also need resources to help needy families send their children to college, which many cannot afford to do - let along enabling them to pursue advanced degrees.
"Education is key for every nation trying to transform society."
One of the fears many Islamic extremists have in Pakistan is that Christians have been influenced, or will be, by the west.
"If the West strikes against Muslims anywhere in the world, enraged fundamentalists in Pakistan often attack the churches," the bishop explained.
He added that moderate Muslims and other religious minorities are at risk too.
"There are far more attacks on mosques than on churches - fundamentalist Muslims killing moderate fellow Muslims."
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.