Davis, who has two years left on the six-year, $42.7 million contract he signed in 2010, has been absent as he's seeking a new deal, according to a report by CSNBayArea.com.
He is forfeiting a $200,000 workout bonus by not showing up.
When asked about Davis' absence, coach Jim Harbaugh told the media that workouts were voluntary.
Davis was drafted sixth overall by the 49ers in 2006. He was a Pro Bowl selection last season after making 84 catches for 850 yards and 13 touchdowns.
The 49ers' ability to re-sign or restructure Davis' deal could be hindered by their need to re-sign quarterback Colin Kaepernick and wide receiver Michael Crabtree, whose contracts are up at the end of the 2014 season.
ESPN.com 49ers reporter Bill Williamson contributed to this report.