Messi, 29, is out of contract in 2018 and is yet to renew, with talks seemingly progressing slowly.
Hazard out of Belgium squad
The delay appears to have had little impact on the form of Messi, who has already scored 41 goals – matching his tally from last season – in all competitions.
Despite the wait, Fernandez said he remains certain the Argentina star will commit to Barcelona.
“Messi will renew,” he told Cadena SER on Monday.
“I have always said Leo is happy in Barcelona. He is very happy here, he is in a magnificent team.
“I have no doubt that he will renew.”
Fernandez’s comments about Messi come a day after the director said midfielder Andres Iniesta, also out of contract in 2018, will remain at Barca for several more years.