Justice Minister Jeannot Kouadio Ahoussou said the remains were found in the western region of Issia, but he did not provide further details.
Guy-Andre Kieffer, who was 54 when he disappeared, was working in the commercial capital, Abidjan, as an independent journalist, writing articles about corruption in Ivory Coast.
He was a dual citizen of France and Canada.
Reporters without Borders said in a statement that a skeleton was discovered after French judge Patrick Ramael ordered a search in the area to advance the investigation.
The group said DNA results are expected within a week.
Even if the body is confirmed to be Kieffer's, the mystery of his disappearance and death remains.
"If the bones found are those of Guy-Andre Kieffer, confirming that the journalist was murdered and buried after his abduction, it remains to be seen who the perpetrators are. Who exactly abducted the journalist? Who killed him and why?" said the statement the group.
Kieffer's family has maintained he was targeted by the government of former president Laurent Gbagbo for his reporting, and says he spent two days in a jail cell at the presidential palace after he went missing.
The former government denied any involvement in his disappearance.
His family said elements in Gbagbo's entourage wanted to eliminate Kieffer after several of his articles claimed that kickbacks from cocoa exports were being used to purchase arms for the civil war against rebels who had taken control of the northern half of the country.
France — Ivory Coast's former colonial ruler — opened an investigation into the case in 2004 and arrested several suspects.
"Until it is confirmed that it is the remains of Guy-Andre Kieffer, it is essential to be cautious, but one thing is certain: this is the first time in nearly eight years that the investigation has gone so far," the group's statement said.