Faye said that France's President Emmanuel Macron had admitted that his country's troops were responsible for a "massacre" of Senegalese soldiers in 1944.
Faye hailed the acknowledgement but said that allowing French bases in the country was incompatible with national sovereignty.
"Senegal is an independent country, it is a sovereign country and sovereignty does not accept the presence of military bases in a sovereign country," Faye said in an interview at the presidential palace.
Faye swept to power in March's elections promising to assert Senegal's sovereignty and an end to dependence on foreign powers.
He however maintained that the act did not constitute a break with France, like those seen elsewhere in west Africa in recent years.
"Today, China is our largest trading partner in terms of investment and trade. Does China have a military presence in Senegal? No. Does that mean our relations are cut? No," he said.
- 'Making amends' -
Several other francophone countries in west and central Africa, including Mali, Burkina Faso and Niger, have been taken over by military juntas that have expelled French forces and turned to Russia for security aid instead.
Two French government sources told AFP this year that the country was looking to cut its military presence in Africa -- from 350 troops to 100 in Senegal and Gabon and to 300 in Chad from 1,000 and 100 in Ivory Coast from 600.
"France remains an important partner for Senegal for the investment for Senegal and the presence of French companies and even French citizens who are in Senegal," said Faye.
Senegal's president said he had received a letter from Macron admitting French culpability for a World War II-era massacre at Thiaroye on December 1, 1944.
The atrocity has long been a bone of contention between Paris and Dakar.
In November 1944, around 1,600 African soldiers who had fought for France and been made prisoners of war by Germany, were sent back to Dakar, according to French historian Armelle Mabon.
Soon after arriving at the Thiaroye camp, just outside Dakar, they protested against pay delays, with some refusing to return to their home countries without their dues.
French forces opened fire on the protesters, killing at least 35, though historians say the toll could be much higher.
"I received today a letter from President Emmanuel Macron in which he acknowledges that it was a massacre, very clearly, unambiguously on the terms," Faye said.
He praised "a great step" taken by the French leader, who Faye said apologised for not being able to make the commemoration of the massacre's 80th anniversary.
Faye said he was considering demanding an apology from France.
"To recognise that a massacre has been committed must obviously have the effect of making amends.... we think that naturally this is what must follow."
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