The Pope has criticised Muslims for imposing their religious laws on Christians in Nigeria.
He told a meeting of Nigerian Catholic bishops he supported and encouraged their fight against the Islamic code.
Muslims in some areas of Nigeria are imposing their version of Sharia, or Islamic religious laws, on the whole population.
Pope John Paul II said everyone in Nigeria should enjoy the freedom of religious expression. He said all citizens should be equal before the law, whatever their beliefs.
It is the first time the Pope has spoken out over the division between Muslims and Christians in the country. He made the statement while addressing the Bishops in the Vatican during their visit to Rome.
He told them: "I strongly encourage and support your every effort to speak out courageously and forcefully in this regard."
The Holy Father said the cultural and ethnic plurality in Nigeria should be a source of enrichment for the nation, not a cause of conflict and rancour.
On the 2003 general elections in the country, the Pope advised the bishops to intensify ecumenical and inter-religious co-operation to ensure a free and peaceful polls.
A Nigerian mother was recently narrowly saved from being stoned to death after allegedly committing adultery. An international human rights campaign forced the local authorities to step in.