The government will file the lawsuit “in the next few days,” the minister, Arturo Murillo, told state radio Patria Nueva.
The International Criminal Court sitting in The Hague has jurisdiction to prosecute individuals for crimes against humanity.
Murillo last week filed a criminal complaint in Bolivia accusing Morales of sedition and terrorism, after he allegedly called on supporters to blockade cities and cut off fuel and food supplies.
The ex-president “must answer to justice for what he has done, and is doing, in addition to his accomplices who have participated in the tragic events that Bolivians have experienced,” Murillo said.
If Morales — who fled to Mexico after resigning on November 10 — were charged and convicted in a Bolivian court, he would face a maximum penalty of 30 years in jail.
Morales has in turn accused the interim government of “genocide” following the deaths of 32 people, mostly his indigenous supporters, in post-election violence.
Morales denied wrongdoing and said he was being persecuted for leading a pro-poor, pro-indigenous government and nationalizing the country’s gas and other natural resources.
Congress last week gave a green light for a new vote without Morales, Bolivia’s first indigenous president. He had been seeking a fourth term after nearly 14 years as leader of the poor but resource-rich country.
Meanwhile, Murillo expressed concern over the presence in the country of an Argentine human rights group.
“We recommend these foreigners who are arriving….to be careful,” said Murillo. “We are looking at you. We are following you,” he said in the radio interview.
“There is no tolerance for terrorism, sedition or armed movements. Zero tolerance,” he said.
The Argentine rights delegation tweeted: “While the de facto government accuses us of being terrorists, we have started what we came to do, take testimony of the different human rights violations that the Bolivian people are enduring.”