The Ghanaian ambassador heard of Burkina's "disapproval" of the president's claim that Ouagadougou had struck a deal with the controversial paramilitary outfit, the ministry said.
"Ghana should have sought to exchange with the Burkinabe authorities on the security question in order to have the right information," minister for regional cooperation Karamoko Jean Marie Traore told Ghana's envoy, according to a foreign ministry statement.
Ghana's ambassador Boniface Gambila Adagbila said his president "did not intend to condemn Burkina Faso, nor to sow doubt", according to the statement.
"The intention was above all to draw the attention of partners to incite great interest in Burkina Faso," he was quoted as saying.
The claim was "serious and inexact", a Burkina Faso government source told AFP, adding that Burkina's ambassador in Accra had been recalled for consultations.
Ghana's President Nana Akufo-Addo on Wednesday accused neighboring Burkina of striking a deal to deploy mercenaries from Moscow's Wagner Group, calling it "particularly distressing."
Akufo-Addo had said: "Burkina Faso has now entered into an arrangement to go along with Mali in employing the Wagner forces.
"I believe a (mineral) mine in southern Burkina has been allocated to them as a form of payment for their services," he said during a meeting with US Secretary of State Antony Blinken.
"To have them operating on our northern border is particularly distressing for us in Ghana."
Rekindling ties with Russia has also been on the agenda in Burkina since a September coup, the second in eight months, which brought Captain Ibrahim Traore to power facing jihadist attacks that have haunted the country since 2015.
On Monday, Burkina Prime Minister Apollinaire Kyelem de Tembela met Russian Deputy Foreign Minister Mikhail Bogdanov in Moscow to discuss "the priority issues of strengthening relations", the Russian foreign ministry said.
