In a statement the Holy See criticised a "artificially created fear of Muslims."
The Vatican has said that Poland has not encountered much immigration and remains "ethnically homogenous".
"The phenomenon of immigration in general (and of refugees and asylum seekers in general) is new, different, and strange to the average Polish person," according to the statement.
It also said that a lack of public debate, as well as no government teaching about tolerance have not helped the problem.
It does thank some Polish people for welcoming their new neighbours, but admits that more could be done to integrate and accept others.
The Vatican goes on: "We must not lose sight of the main reason for the current migratory crisis, that is, wars in the Middle East and in Africa.
"From this there arises the need to pray for peace, to continue efforts at mediation and to appeal tirelessly to the conscience of governors.
"Many people have remained in their own countries, and there they await the arrival of aid directly in the afflicted regions. At the same time we must take care of those who have decided to leave the land of their ancestors.
"We ask the faithful of our Churches to pray and give assistance to those in need. We cannot abandon the search for solutions to the current crisis."
Pope Francis arrives in Poland next week for World Youth Day celebrations.
The event, which millions are expected to attend, is celebrated every three years in a different country.
This year it is being held in Krakow, Poland and some argue there is a tension between the pope and the nation after Pope Francis made welcoming refugees and those in need a key part of his message to Catholics.
The Polish government has yet to accept its European Union quota of new comers.
