The team said Balmer met Wednesday night with coach Mike Singletary.
Singletary allowed Balmer to miss Monday and Tuesday workouts as he dealt with a "personal issue." But the 49ers had expected him back Wednesday.
Balmer, San Francisco's first-round draft pick in 2008 out of North Carolina, is entering the third year of the five-year, $8 million deal he signed as a rookie. He has yet to start a game and recorded no sacks in his first two NFL seasons.
Later Thursday, the 49ers signed rookie free agent defensive tackle Will Tukuafu to a two-year contract to help fill the void left by Balmer's absence. Tukuafu, out of Oregon, was originally signed by the Seattle Seahawks before they released him June 22.
Defensive coordinator Greg Manusky acknowledged the Niners are looking to bring in someone to play defensive end to fill the void left without Balmer -- perhaps in time for Sunday's exhibition opener at Indianapolis.
"Kentwan is kind of a different situation. Coach Sing deals with that," Manusky said. "I coach the players who are here on the practice field. That's my job. You see the job analysis and that's what I do: Coach the guys who are out here. I don't know what's going on with him, but from an adjustment standpoint, we're going to bring another lineman, a person who can play defensive end for us."