The gift combining Catholic and communist symbols has caused a stir among Catholic commentators.
One Catholic bishop suggested that Evo Morales had sought to “manipulate God”.
While some reports said Pope Francis was taken aback by the present, the Vatican has played down any row.
The crucifix was based on a design by Luis Espinal, a Jesuit Priest assassinated in 1980 by right-wing militia.
Bolivia’s communications minister, Marianela Paco, told Bolivian radio: “The sickle evokes the peasant, the hammer the carpenter, representing humble workers, God’s people.”
She added there was “no other” motive behind the gift.
There are differing interpretations of Pope Francis’ thoughts on it.
Some reports say Pope Francis was embarrassed, telling Evo Morales: “This isn’t good.”
However, the Vatican spokesman, Federico Lombardi, said it was more likely Pope Francis had expressed surprise at the origins of the gift.
“I don’t think I would put this symbol on an altar in a church however,” he added.
Pope Francis himself has been accused of having Marxist leanings, after mounting strong criticisms of capitalism and inequality.
One of the strongest reactions came from Spanish bishop Jose Ignacio Munilla, who tweeted: “The height of arrogance is to manipulate God for the service of atheist ideologies.”
“This is a provocation, a joke” said Bolivian Bishop Gonzalo del Castillo, quoted by the AFP news agency.
There was also anger on the Facebook pages of the Catholic News Agency.
Pope Francis is now in Paraguay, the third and final country on his tour of Latin America, which ends on July 13.
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