When he died a mob tried to throw his body into the River Tiber.
Both are now on the path to becoming saints of the Catholic church.
"I would expect the Vatican to show greater sensitivity towards believers from other faiths," said Michael Melchior, Israel's minister for the diaspora.
Forced conversion
Pope Pius IX confined Rome's Jews to a ghetto and forcibly baptised their children as Christians.
He allegedly referred to Jews as "dogs".
When he died a mob tried to throw his body into the River Tiber.
Mr Melchior said that the beatification of Pope Pius was equivalent to giving support to "the Roman Catholic Church's historical record of forced conversions."
Jewish groups also voiced their protests. The New York-based Anti-Defamation League called the beatification "troubling".
"I am very disappointed by this," said Rabbi David Rosen, head of the International Jewish-Christian Association.
Veneration for virtue
Pope John Paul acknowledged the controversy in his decision, saying Pope Pius IX was "much loved, but also hated and defamed."
"Beatifying a son of the church does not celebrate particular historic choices that he has made, but rather points him out for imitation and for veneration for his virtue," he said.
He stressed Pope Pius IX was faithful to "the duties of his ministry, and always gave God and spiritual values absolute priority."
Pope John Paul also beatified John XXIII, who died in 1963, and is seen as a great reformer.
Two very different popes
In his homily, Pope John Paul praised both his predecessors as loyal servants of God.
John XXIII convened the Second Vatican Council which revolutionised the Catholic church.
He is also popular among Jews for helping some of them escape Nazi persecution.
The BBC's Rome correspondent, David Willey, says the decision to beatify at the same time two former pontiffs with such different records could send out a confused message.
Piux IX listed 80 propositions which he condemned as erroneous, including socialism, liberalism, communism, rationalism, progress and modern civilisation in general.
John Paul II has undertaken more than 1,000 beatifications and canonisations - more than any of his predecessors.