The world and European champions are looking to secure the long-term future of the Brazilian star amid reported interest from archrivals Real Madrid.
The player's father grabbed headlines during Neymar's 24th birthday party on Friday after he clashed with journalists, insisting they should leave him alone.
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Barca issued a statement shortly afterwards, demanding respect from Spanish media, and Fernandez insists the attacker is happy at the club, as is his father.
"Neymar and his management are very happy and we are very relaxed," he told Marca.
"The club stands by the player. These things happen and we shouldn't dwell on it.
"The important thing is that he is happy and that's something we can see in every game he plays."
Sunday's 2-0 win over Levante ensured Barca remain three points ahead of Atletico Madrid and a further point ahead of Real Madrid, though the Catalans have a game in hand over their rivals.
And Fernandez was delighted to see Luis Enrique's men emerge triumphant despite difficult conditions.
"It was a difficult game because the weather was not good. What bothers the player is the wind. But the team was solid against an intense rival. We have to be satisfied.
"We have to keep working and playing well."