Mr Morales said Catholic leaders should understand the need for freedom of religion and belief.
His government recently announced plans to teach a range of religions in schools, as well as native traditions.
Church leaders have opposed the planned changes, calling on Catholics to defend their faith.
"I want to ask the [Church] hierarchies that they understand freedom of religion and beliefs in our country," Mr Morales said.
"It's not possible to impose their views. I am very worried by the behaviour of some Catholic Church leaders, who act like in the time of the Inquisition."
He insisted Bolivia would continue to respect the Church.
He spoke out after Catholic leaders criticised the planned reforms, which would break the long-standing dominance of Catholicism in Bolivian schools.
'Liars'
The archbishop of Santa Cruz, Cardinal Julio Terrazzas, said on Sunday that Catholics were being "passive" in the face of Mr Morales' planned changes.
"Great wars begin with small theories... with this discourse of hate, of rancour, of unforgiveness," he said.
On Sunday the country's education minister, Felix Patzi, said Catholic leaders were "lying" over claims that the government was aiming to destroy the Church.
However, he said the planned changes would allow Bolivians to break down "ethnic borders" that have marginalised native traditions for more than 500 years, the Associated Press reported.
A majority of Bolivians describe themselves as Catholic, according to census figures.
After the Roman Catholic Church consolidated its power across Europe in the 12th and 13th Century, it set up the Inquisition to ensure that heretics did not undermine that authority.
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I actually let out a little cheer when I read this.