A person familiar with the situation also confirmed the meeting to The Associated Press, speaking on the condition of anonymity because of the sensitive nature of the talks.
McNeill, a two-time Pro Bowl left tackle, requested the sit-down, sources told The Union-Tribune, so he could better understand where the team stood on his contract. Smith has been steadfast in his stance against giving McNeill a new deal, saying in July that he had "nothing to discuss" with the left tackle and Pro Bowl wide receiver Vincent Jackson, who's also holding out from training camp.
"As I've said before, I'm done talking about Marcus McNeill until he returns," Smith said Wednesday when asked about the meeting. "If he does return, I would be more than happy to talk about him."
McNeill's agent, Alvin Keels, wouldn't confirm to the newspaper that his client met with Smith. McNeill, Keels and Smith didn't immediately return calls and e-mails from The AP seeking comment.
Keels confirmed to The AP last week that the Chargers have threatened to place McNeill on the roster exempt list if he doesn't sign his one-year tender by Friday. If he goes on the roster exempt list, McNeill couldn't play in the next three games after he signs.
Jackson, who also was offered a one-year tender, could be placed on the roster exempt list as well if he doesn't sign. He also has been suspended by the NFL for the first three games of the season for violating the league's substance-abuse policy.
McNeill and Jackson, who want long-terms deals, are believed to be willing to sit out the first 10 games of the season, returning for the final six in order to accrue a season toward unrestricted free agency. However, being placed on the roster exempt list would force them to move up their returns, if they intend to play at all this year.
As restricted free agents, Jackson was tendered at $3.268 million and McNeill at $3.168 million. They didn't sign by the June 15 deadline, so they each forfeited approximately $2.5 million because the Chargers exercised their right to lower the tenders.
Linebacker Shawne Merriman ended his holdout last Friday when he signed his restricted free-agent tender and practiced.
Notes: Merriman sat out Wednesday's practice with a sore Achilles' tendon, but he said the injury wasn't serious and he could return to practice this week or early next week. It's doubtful he'll play in Saturday night's preseason home game against the Dallas Cowboys. ... Among others not working out were LB Brandon Siler (ankle), OL Tyronne Green (ankle) and CB Donald Strickland (hamstring). ... LT Tra Thomas, who's returning from a recent arthroscopic knee surgery, continued to impress in his second day of team drills. With the Chargers desperate at left tackle because of McNeill's holdout, coach Norv Turner is upbeat that Thomas, a 13-year pro, will be able to bounce back quickly. "It's clear he still has plenty of ability and he is an excellent pass-protector," Turner said. ... The NFL granted the Chargers a 24-hour extension in an effort to sell enough tickets to lift the local TV blackout of Saturday's game. The team has until 6 p.m. Thursday to sell the remaining 1,000 tickets.
The Associated Press contributed to this report.