SANTA CLARA, Calif. — The San Francisco 49ers were only missing two healthy players at their first practice of training camp on Wednesday. But the two not in attendance also happen to be two of their best and were not participating for the same reason: contract disputes.

In addition to receiver Brandon Aiyuk, who reported on time Tuesday and is at the facility but not practicing (a “hold-in”), the Niners are also without star left tackle Trent Williams. Unlike Aiyuk, Williams did not report for camp and is holding out for what coach Kyle Shanahan described as “contract-related” issues.

“It was something I knew could be a possibility and I was hoping that he would be here,” Shanahan said. “But I knew it could be a possibility and I felt pretty confident it’ll all work out in the long run and he’ll be here, and we’ll get on the same page with everything. But it’s just one day of practice and I think Trent will be all right missing a few practices.”

There were signs that Williams might be unhappy with his contract as far back as the spring. Shanahan said that general manager John Lynch and Williams’ representatives began discussions around that time, though Williams did show up in Santa Clara for part of the team’s mandatory minicamp. He was excused for the other part because his daughter was finishing her school year.

Still, Williams is in a similar boat to where running back Christian McCaffrey was before he signed a reworked contract extension in early June. Like McCaffrey, Williams has multiple years (three in his case) remaining on the six-year, $138.06 million deal he signed with the Niners in 2021.

Also, like pre-extension McCaffrey, Williams’ deal includes no more guaranteed money, though the Niners are still on the hook for nearly $30 million in signing bonus proration through 2027 because of restructures they’ve done on the contract.

In the time since signing, Williams has also fallen from his perch as the game’s highest-paid offensive lineman. Minnesota Vikings tackle Christian Darrisaw ($28.25 million per year), Detroit Lions tackle Penei Sewell ($28 million per year), Houston Texans tackle Laremy Tunsil ($25 million per year) and the Giants’ Andrew Thomas ($23.5 million per year) have all surpassed Williams’ $23.01 million annual average despite Williams still ranking as the best pass blocking tackle in the NFL in 2023 (95.8% pass block win rate).

Williams is still regarded as the game’s most dominant lineman and was selected to his 11th Pro Bowl last season, the most among active players. He also has been selected as first-team All-Pro in each of the past three seasons. Veteran Jaylon Moore took the snaps at left tackle in Williams’ stead on Wednesday.

If the Niners do what they did with McCaffrey, a reworked deal for Williams, 36, is likely to include guaranteeing a large chunk of the money already owed to him over the next couple of seasons, as well as tacking on money on the back end that would bolster him back to at or near the top of the tackle market.

Because he’s long-since removed from his rookie contract, Williams is subject to fines of $50,000 per day for every practice he misses. Those fines cannot be forgiven by the Niners, according to the league’s collective bargaining agreement.

Williams’ contract squabble comes in the midst of the ongoing saga with Aiyuk, who is entering the final year of his rookie contract and has been seeking a lucrative extension all offseason.

In a bit of a surprise, Aiyuk reported to training camp on time Tuesday. And though Lynch said he expected all healthy Niners present to participate, it was no surprise that Aiyuk was watching from the side in shorts and a T-shirt on Wednesday. Because Aiyuk is “holding in,” he’s not subject to fines.

Aiyuk took in the first few minutes of practice and was seen walking and talking with Lynch for a bit before departing the practice fields. Shanahan said Aiyuk is dealing with neck and back soreness as well but acknowledged that Aiyuk is unlikely to practice without resolution to his contract situation.

“It’s what we expected, and we understand the situation fully,” Shanahan said.

The Niners’ contract-related issues can be traced to the team’s success and the number of top-end players that dot the roster. While McCaffrey, Aiyuk and Williams have been the focal points this offseason, there are plenty of other money issues in the offing.

Cornerbacks Charvarius Ward and Deommodore Lenoir, linebacker Dre Greenlaw, guard Aaron Banks and safety Talanoa Hufanga are among the key players set to be free agents after this season.

And in what is expected to be the most expensive contract of all, quarterback Brock Purdy is eligible for an extension for the first time next spring.

“We understand the business side of it,” linebacker Fred Warner said. “This isn’t our first rodeo. This is a curse and a blessing to have this many great players part of our team. We’ll get it figured out.”