The Mali government statement said that President Faure Gnassingbe had been "welcomed" by junta leader Assimi Goita before heading for "a working session" at the Koulouba Palace presidency.
Malian authorities detained 49 Ivorian soldiers after they arrived at Bamako airport on July 10 to provide backup security for a UN peacekeeping mission.
Three women soldiers were freed, but later sentenced to death in absentia.
The troops were found guilty of an "attack and conspiracy against the government" and seeking to undermine state security, public prosecutor Ladji Sara said in a statement last month.
A Malian court last month sentenced the troops, accused of being "mercenaries," to 20 years in prison, despite a threat of sanctions from West African leaders.
The West African bloc ECOWAS had given Mali a deadline of January 1 to free the troops or face sanctions. However, it has remained mum since the December 30 sentencing.
In his New Year's address, Ivorian President Alassane Ouattara promised that the imprisoned soldiers "will soon return to Ivorian soil".
"We must trust the head of state," Ivorian government spokesman Amadou Coulibaly said after a cabinet meeting on Wednesday.
"Ivory Coast has chosen a way - that of negotiation - it is the diplomatic way, we remain resolutely committed to this path," he added.
He declined to comment on the convictions of the Ivorian soldiers.
"We never comment on court decisions taken in Ivory Coast; there is no reason for us to comment on court decisions taken abroad," he said.
Ivory Coast has categorically denied the soldiers were "mercenaries" and insists that they were on a mission for the UN to provide logistical support for its MINUSMA operations.
On December 22, an Ivorian delegation visited Bamako to discuss the detention of the soldiers.
At the end of that visit, a memorandum was signed and Ivorian Defense Minister Tene Birahima Ouattara said the matter was "on the way to resolution".
The agreement leaves the door open for a possible presidential pardon by Goita, who did not mention the Ivorian soldiers in his end-of-year speech on Saturday.