The club insists the 29-year-old All Australian will play in Friday night's Grand Final rematch against Hawthorn at the MCG.
Match Preview - Fremantle v Hawthorn
Johnson's role will be vital, particularly following Zac Dawson's suspension.
"He'll come across today; he's obviously missed the flight for personal reasons, but we're confident he'll be fine," assistant coach Michael Prior said on Thursday.
"They're professional athletes these days, so we've got full faith that he'll be fine.
"I'm his line coach, so we'll make sure we cover off all that needs to be covered off."
The reason for Johnson's late departure has not been made public.
Ross Lyon comments on Johnson's late departure
Prior said he had taken part in match preparations throughout the week.
"He's done the training so he's ready to go, there's no issue there.
"They [Hawthorn] obviously have some good key forwards and Johnno's going to have to play on one of them, so he'll have his head right by game time."
Johnson was yet to arrive when Fremantle players took a dip in the icy waters of Port Phillip Bay on Thursday morning.
The Dockers will also be without star midfielder Nat Fyfe, who was suspended for two weeks over a head clash in last week's game against Gold Coast.
Fyfe, Dawson accept bans - Barlow out
