"Monsignor Michele Russo has arrived here in Rome," a member of the Comboni missionary congregation told AFP.
An airport official in Chad earlier said he had left the country on a flight via Paris.
The government on Friday announced the expulsion of Russo, who has been bishop in the oil-rich southern Doba region for 23 years and has campaigned for ordinary people to receive a much greater share of Chad's new oil wealth.
Chad authorities said a sermon delivered by the 67-year-old Russo and broadcast by a private radio station was "likely to disturb public order" and that the bishop had "engaged in activities incompatible with his status".
The Vatican missionary news agency Fides on Saturday quoted Church sources in Chad saying that Russo's words had been mistranslated by the radio station, adding that the government of Chad appeared "open to dialogue" on the case.
Chad's conference of bishops has expressed "great sadness" over the expulsion of the prelate, saying in a statement that it "regrets this situation that is without precedent in the history of the Catholic Church in Chad".
Russo's small diocese has 10 parishes and some 400,000 inhabitants, of whom around 20 percent are Catholic. A majority of Chadians are Muslim.
A member of the Comboni congregation, Giulio Albanese, told Vatican Radio: "Behind all this, according to some observers, there are the interests of local politicians and oil companies, which have been suspicious of him for a while."
Russo has long been critical of the government of the country that began producing oil in 2003 and in a statement to Fides earlier this month he said Africa's natural wealth had been mismanaged for decades by "human greed".
"The riches, because of human greed, have turned from blessing into curse for the local population," he said. "The natural wealth of Africa should be used to build the future of the daughters and sons of the continent."
"After 50 years of uncontrolled exploitation, with the complicity of local governments and indifference towards the African people and their future, I think it's time to become aware of these facts," he added.
Chad produces on average around 120,000 barrels per day, according to government estimates from 2011.
Oil revenue has allowed the poverty-stricken central African country to modernise its army, upgrade its roads and build numerous public buildings.
But there has been criticism of the government in some quarters for not doing enough with the windfall to better the lives of ordinary Chadians.
In an interview with the Italian development website Negrizia in 2009, Russo said that local society had "come apart" since Chad began producing oil.
He accused major powers of "robbing" Chad, the government of "selling the country" and the population of misusing the "crumbs" of oil revenue left over.