Johnson strained the medial ligament in his right knee against Adelaide in round 12.
Luke McPharlin suffered the same injury in the same game but returned to face Melbourne last week.
Lyon said Johnson needed to get through training this week before he was declared a certain starter against Greater Western Sydney on Sunday, and he trained fully on Wednesday.
The Dockers coach said it was important that his All Australian defender did not miss a fifth week at this stage of the year.
"You don't want to miss too much of league footy," Lyon said.
"It's a brutal competition. We've still got match committee … but he's obviously a valued leader around the place and a real general down there. So we're keen to get him up and going."
The Dockers have been stretched in defence in recent weeks due to the injuries of McPharlin, Johnson, and Alex Silvagni, who is still unavailable after suffering a collapsed lung.
Zac Dawson was absent for large parts of Wednesday's open session although the tall defender is regularly managed during the week.
Matthew Pavlich is due to return after missing with illness last week.
Lyon said that youngster Michael Apeness would certainly play after a strong performance on debut in Darwin.
"I thought he was really good," Lyon said.
"It was tough conditions. He's a bit of a beast. He competes.
"We're looking for that in our front half, so he has an opportunity again this week, I would think. You can probably bank it in that he's going to play."
One man who won't play on Sunday is Stephen Hill.
The Fremantle wingman has been in outstanding form this season, but he injured his quad at training last week and will miss another two weeks after being withdrawn from the clash with the Demons.
Hill missed four weeks last year with a similar quad injury and Lyon said it was imperative that he recovered well given his value to the side in September.
"Clearly if he has done it twice it's something we've got to be mindful of, and he's got to be mindful of," Lyon said.
"We'll put a strength program in place, but they can be tricky injuries. This is at the minor, minor end but we will take the full three weeks to get him right because he is so valuable."
