Singletary gave Balmer a pass Monday and Tuesday to deal with a "personal issue." Wednesday's absence was unexcused.
"I told Kentwan to be here this morning," Singletary said. "He's not here. He is under contract. The fact that he's not here, that speaks to me. What it says, I really don't know. As far as I'm concerned, I don't know what he's doing."
Balmer told the San Jose Mercury News he has a meeting scheduled with Singletary on Wednesday and plans to return to the 49ers. He also echoed the team's stance that his absence was a personal matter.
"People are making a big deal about of nothing," Balmer told the newspaper. "I feel like the 49ers could do a better job of saying that, but it's not my place to say."
Balmer, San Francisco's first-round draft pick in 2008, is entering the third season of the five-year, $8 million deal he signed as a rookie.
The defensive lineman from North Carolina has been a disappointment so far to the 49ers and was battling just to make the roster this summer. He has yet to start a game or record a sack in his two seasons with the team.
Balmer finished last season on injured reserve after missing San Francisco's final five games with a torn labrum. He declared himself healthy at the start of training camp, but has fallen down the depth chart this summer behind starters Justin Smith and Isaac Sopoaga and veteran backups Ray McDonald and Demetric Evans.
Singletary said the 49ers would "probably have to bring in another player" along their defensive line. The team also is practicing without Aubrayo Franklin, who spearheaded San Francisco's 3-4 defensive scheme last season from his starting nose tackle position.
Franklin had a career season in 2009, and the 49ers designated him as their franchise player in March. Franklin missed all of San Francisco's offseason workouts and has remained absent during training camp as he seeks a new contract. He has yet to sign the team's one-year tender offer of $7.003 million and may not arrive until the end of this month.
Smith, the veteran leader of San Francisco's defensive line, said the unit already has adjusted to the absence of both Franklin and Balmer.
"We're moving along," Smith said. "Whatever the situation may be, in football you're used to people going down so it's no big deal. You just roll with what you've got."
Balmer's name has surfaced recently in news reports of an NCAA investigation at North Carolina, which Balmer attended.
The investigation has no impact on Balmer's NFL career, and the 49ers don't believe it has anything to do with Balmer's absence. A 49ers spokesman said the team is now following standard procedure for a player who has left camp, indicating Balmer will be fined for any further absences.
Singletary gave a cryptic response when asked if Balmer was jeopardizing his future with the 49ers.
"I don't want to go there," Singletary said. "I'm done with Kentwan. I'm done. There is not going to be any phone calls [to Balmer]. I don't want to say anything further than that. We're doing what we have to do. I don't want to talk anymore about something that's not here."
Rookie LB NaVorro Bowman missed practice for the third consecutive day with a shoulder injury. ... LB Travis LaBoy remains out with a concussion suffered early last week. ... Singletary said first-round draft picks Anthony Davis and Mike Iupati, who both were promoted to starting positions on the offensive line, may play more than the other starters in Sunday's exhibition opener at Indianapolis. ... Second-year linebacker Scott McKillop was waived. McKillop tore ligaments in his left knee during practice Aug. 4 and had season-ending surgery two days later. If he clears waivers, he will be placed on San Francisco's injured reserve list. ... Linebacker Martail Burnett was placed on injured reserve after he cleared waivers. Burnett injured his knee earlier this week. ... The 49ers signed rookie free agent receiver Bobby Guillory to a two-year contract and waived rookie receiver Scott Long.
Information from The Associated Press was used in this report.