The defender, who won the Under 19 Euros with Spain in 2012, has made 28 La Liga appearances this season and has also been a regular in Valencia's march to the Europa League semi-finals and his bright performances have seen him linked to the likes of Manchester United and Napoli.
Valencia's well-documented financial problems have seen them sell many of their best players in recent years, with David Silva, Juan Mata, David Villa and Roberto Soldado all leaving the club for big-money fees.
But Rufete, says Valencia are determined to keep Bernat - who can also play on the left side of midfield - in Spain, despite foreign interest.
"Juan is a home-grown player from our academy and is a very important player for us," Rufete is quoted as saying in the Italian media.
"We want him to stay with us for a long time, but we also know that there are many clubs that are interested in him because he is playing at such a good level.
"It is good that the team continues to produce such results and Bernat is certainly a player that interests Napoli and many other clubs, but our intention is to keep him."