Johnson was absent from Freo's main training session on Wednesday morning and did not fly with the team but Lyon said the All Australian backman would line up against Hawthorn.
"He's not travelling today - he's got a personal matter but we expect him to play," Lyon said.
"He trained earlier in the morning.
"He's a very important player to us. Barring mishap I’d expect Michael to be playing."
After already losing Nat Fyfe and Zac Dawson to suspension, and Michael Barlow to a knee injury, the Dockers could ill-afford to lose Johnson as well.
The club is keeping its options open, with 23 players flying to Melbourne on Wednesday.
Clancee Pearce, Garrick Ibbotson, Zac Clarke, Lachie Neale, and Hayden Crozier all travelled, along with 18 of their teammates who played in Fremantle's 48-point win over Gold Coast last Saturday.
The Hawks have some injury concerns of their own, with premiership stars Luke Hodge (groin) and Sam Mitchell (calf) in doubt.
Lyon believes it is a great opportunity for some of his young players to stand up.
"We understand we're playing the premier team in the competition," Lyon said.
"Like us, they have got a few challenges with personnel. But like us the best teams and the best clubs use no excuses and expect the next person in to deliver. We'll be the same.
"Clancee Pearce, Lachie Neale, Garrick Ibbotson, Zac Clarke, all those kind of guys, we expect them to be able to deliver. It's a wonderful opportunity for us all."
Lyon said the Dockers could cover the loss of Fyfe and Barlow in the midfield. The pair combined for 61 disposals, eight clearances, and two goals against the Suns.
"Matt de Boer’s been going through – we’ve had enormous numbers through there," Lyon said.
"Michael Walters, Lachie Neale should play I would think."
Lyon said it was important for the Dockers to take their opportunities against the Hawks in light of what happened in last year's Grand Final, when Freo frittered away numerous opportunities before losing by 15 points.
"It’s always important to grab the opportunities," Lyon said.
"At the end of the day, there’s physical pressure and there’s scoreboard pressure.
"We’d like to get off to a good start. The best teams start well, and the best teams tend to win first quarters – it’s hard to come from behind, we all know that.
"It will certainly be an aim to start well and kick straight."
