Messi agreed a new deal until 2021 last month, but the five-time Ballon d'Or winner is yet to officially put pen to paper.
The news has raised questions over Messi's future at Camp Nou following Neymar's world-record move to Paris Saint-Germain and linked the 30-year-old — who was expected to sign his extension during pre-season — with a switch to Manchester City.
But Fernandez allayed those fears following Barca's season-opening 2-0 win over Real Betis in La Liga.
"The agreement with Messi is total," Fernandez told beIN Sports .
"We are just looking for the right time for the signature."
Messi was in the thick of the action as Barca — who held a minute's silence to honour the victims of Thursday's terrorist attack in the city — kicked-off the La Liga season with three points thanks to Sergi Roberto and an Alin Tosca own goal.