"We're going to do the best thing we can for the organization and for Brandon," McDaniels said before the meeting. "If those two things are the same, then it will work out. That's what we're attempting to do right now."
The meeting included Marshall's agent as well as team owner Pat Bowlen.
After the meeting, Bowlen told ESPN's Ed Werder that he has a good relationship with Marshall and said, "I'm very keen on having Brandon play for the Broncos."
Marshall is due $2.2 million this season, the final year of a four-year contract he signed as a rookie.
He drove away from the team's training complex after about 1 hour, 15 minutes but didn't stop to speak with reporters.
Marshall also missed part of the Broncos' optional passing camp earlier this spring after hip surgery, but his agent, Kennard McGuire, said at the time it wasn't a ploy to seek a contract re-negotiation.
McGuire didn't reply to an e-mail seeking comment Friday.
Werder reported that McDaniel said Marshall would be fined for his absence, which could cost the receiver up to $9,070 if he misses the entire mandatory minicamp.
It was McDaniels' second faceoff with a high-profile player. Quarterback Jay Cutler became disenchanted when he learned the team had talked about trading him. When McDaniels and Bowen were unable to patch things up with Cutler, they traded him to the Bears.
Asked Friday if he thought the Broncos could settle things with Marshall, McDaniels said: "Whether this does or doesn't get fixed is something that's going to play out in the future."
Because of the surgery, Marshall had not been expected to work out during Friday's minicamp, but team officials said he was required to attend meetings and work with medical personnel.
The Pro Bowl receiver has caught 226 passes for 2,899 yards and 15 touchdowns during his three-year Denver career. He's had at least 100 receptions each of the last two years.
Marshall recently avoided legal and league problems over his March 1 arrest this year in Atlanta on misdemeanor battery charges stemming from a fight with his fiancee.
The charges were dropped last week when both Marshall and his fiancee, Michi Leshase Nogami-Campbell, refused to testify against each other. Earlier, the NFL decided against any punishment.
However, he is still facing a trial on two misdemeanor battery charges stemming from a March 2008 arrest involving Rasheeda Watley, a former girlfriend. The trial, which had been scheduled to open June 11, has been postponed until August.
Information from ESPN reporter Ed Werder and The Associated Press was used in this report.