The Pope is to meet President Vaclav Havel and to hold a rally at a Prague stadium. But the bone of contention concerns his plan to canonise a controversial 17th-century priest Jan Sarkander.
The Vatican says Sarkander was martyred for his beliefs by (Protestant) Moravian noblemen who tortured him to death for refusing to betray a confessional secret.
According to Czech Protestants, Sarkander was a ruthless fanatic who actively participated in the violent religious reaction of the early 17th century. They say he was jailed after being implicated in a plot to enlist Polish Cossacks in the anti-Protestant cause shortly after the outbreak of the Thirty Years War in 1618.
"Sarkander is a symbol of intolerance and violence when it comes to faith and conscience," said Milos Rejehrt, a vicar in the Czech Evangelical [Protestant] Church. "He was an active fighter against evangelicals ... and zealous about one thing: his hatred of evangelicals.''
Shortly after Sarkander's death in 1620, the rebellious Protestants of Bohemia and Moravia were crushed in battle by the Catholic Habsburgs and forced to convert to Catholicism.
Nearly 400 years on, the scars still run deep. Protestants plan to boycott tomorrow afternoon's ecumenical service at Prague's Strahov stadium.
Renewed tension between the Czech Republic's Catholics and Protestants comes amid a spell of uneasy relations between the Vatican and leaders of the Orthodox faith elsewhere in Eastern Europe and the former Soviet Union.
But Catholic officials in Prague remain convinced that Sunday's canonisation in the north Moravian town of Olomouc should go ahead.
"In our eyes, Sarkander was a martyr and a hero whose fidelity to Christianity cannot be called into question," said Father Miroslav Fiala, the spokesman of the Czech Bishops' Conference.
For most Czechs, the row isan irrelevancy. Out of a population of 10 million, there are 4 million Catholics, although less than 1 million are active. Active Protestants number only a few hundred thousand.
Interest in the Pope's visit will not be as high as it was in 1990, when his mere presence in Czechoslovakia was a symbol of the break with Communism.