Davis has two years left on a five-year extension he signed in 2010 and now feels like he deserves more.
In a piece he wrote for SI.com's Monday Morning Quarterback column, Davis feels he is worth more money.
"In 2010 I signed a five-year, $37 million contract extension with $23 million guaranteed," said Davis. "It was the biggest contract for a tight end in league history. Four years later, and I'm playing at a higher level than I was then, which brings me to why I'm holding out. It's all about getting paid what you deserve. It's not that complicated. I want the 49ers to win the Super Bowl, and I want to be on the field this summer working toward that goal, but I have to worry about my future first.
"Most of my teammates and many players in the NFL understand that. A few don't. Behind closed doors, they'll say they're all about the team and would run through a brick wall for the organization. But when you look closer, they're doing things to contradict themselves. I can't listen to anyone but my family and my advisors, because those are the people who are going to be there when football inevitably dumps me."
Davis had 52 receptions for 850 yards and 13 touchdowns last season. Since entering the league in 2006, he has 397 catches for 5,201 yards and 53 scores.
Two other 49er players, right guard Alex Boone and cornerback Eric Wright, also were absent for the start of Tuesday's mini-camp. Boone is seeking a renegotiation of his contract as well, while head coach Jim Harbaugh said that Wright is contemplating retirement.