Liberation said its correspondent Agnes Faivre and Le Monde's Sophie Douce arrived in Paris early on Sunday after they were summoned separately for questioning by the military authorities on Friday and later notified of their expulsion.
The two are "journalists of perfect integrity, who worked in Burkina Faso legally, with valid visas and accreditations ... We strongly protest against these absolutely unjustified expulsions," Liberation said in a statement on its website.
There was no statement from the authorities in Burkina Faso about the expulsions, and they did not immediately respond to a request for comment.
On 27 March, the government issued a statement dismissing a Liberation report about alleged killings by the Burkinabe military.
The French foreign ministry did not immediately respond to a request for comment.
Relations between Paris and Ouagadougou have deteriorated sharply since Burkina Faso's military seized power in a coup in September. The junta has since ordered French troops to withdraw from the country and suspended broadcasts by France's RFI radio and television channel France 24.
"These two expulsions mark a new major setback in the freedom to inform on the situation in Burkina Faso," Le Monde director Jérôme Fenoglio said in a statement.
Douce's reporting "obviously ended up seeming unbearable to the regime of Ibrahim Traoré, transition president for six months," he said.
Liberation said its recent investigation into children and adolescents allegedly being killed in a military barracks had displeased the authorities.
"These restrictions on freedom of information are unacceptable and the sign of a power that refuses to allow its actions to be questioned," it said.
The Burkinabe government earlier rejected the article and accused the paper of seeking to discredit the armed forces.
The government said on 27 March it "strongly condemns these manipulations disguised as journalism to tarnish the image of a country of honest men".
Burkina Faso is one of several West African countries and former French colonies battling Islamist militant groups that took root in neighbouring Mali and have spread across the region over the past decade.
Thousands have been killed and more than two million displaced across the Sahel region south of the Sahara despite the presence of foreign troops including from France.
Frustrations over authorities' failure to restore security has spurred anti-French sentiment and helped bring about two military takeovers in Burkina Faso and two in Mali since 2020.
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