Addressing students at Dakar University on Thursday, Sonko also slammed French President Emmanuel Macron for turning a blind eye to political "persecution" in Senegal.
Sonko, a firebrand former opposition leader, was at the center of a three-year stand-off with the government of former president Macky Sall that triggered bouts of deadly unrest.
The prime minister was among a group of opposition politicians freed from prison 10 days before the March 24 presidential ballot under an amnesty announced by Sall, who had tried to delay the vote.
While speaking to the students Sonko said, "cooperation must take into account Senegal’s sovereignty in both the monetary and security fields."
"We must ask ourselves the reasons why the French army still has many military bases in our country and their impact on our sovereignty and our strategic autonomy," Sonko said.
"I reiterate Senegal's wish to determine its course which is incompatible with the entrenched presence of foreign military bases," the prime minister added.
Sonko, who said he was addressing the students as the head of his party and not as prime minister, stressed he sought cooperation with other countries "based on mutual respect and the legitimate aspirations of every nation for sovereignty."
He said Macron's government had failed to denounce Sall's crackdown on opposition protests and dissent which led to dozens of deaths and hundreds of arrests.
Macron had received and "congratulated" Sall at "the worst phase of the repression," Sonko said, adding, "this is an incitement to repression, an incitement to persecution."
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