The dejected Australian star sat with her head in her hands after crossing the finish line at Tokyo's Kasai Canoe Slalom course, realising that gold had yet again escaped her.

The bronze is her second after the same result in Rio, while she won silver as an 18-year-old in London.

Without the penalty, she would have won by 0.77 seconds.

The 27-year-old started Tuesday's final as a raging favourite, with no paddler getting close to her in the qualification round and semi-final.

But she came unstuck early in her run, knocking the fourth gate and then crucially had another error on the penultimate one, each incurring two-second penalties.

Posting a time of 102.73 seconds, the penalties pushed her out to 106.73.

German Ricarda Funk, meanwhile posted a penalty-free run of 105.50 to take gold, with Rio Olympic champion, Spaniard Maialen Chourraut crossing with a blemish-free 106.63.

Fox said she was proud of the way she kept her composure after her early error.

"I think I hit gate four early on ... I fought the whole way down and that's something I'm really proud of - the fight to the finish," Fox told AAP.

"The mistake at the finish was one too many unfortunately and took me out of the gold medal spot."

While the kayak race didn't go to plan, Fox was consoling herself that she at least didn't finish the event empty-handed.

"There's relief to be on the podium, a bit of disappointment to not go down the dream run," the Sydneysider said.

"At the same time to get on the podium with a mistake near the finish line - I've been consistent at the last three Olympics to be on the podium."

Coached by her French mother Myriam Fox-Jerusalmi, who won bronze in the event in Atlanta, her father Richard Fox was a top British paddler and finished fourth at the Barcelona Games.

Working as a commentator on the event, he knew despite the fast time the damage was done.

"That two-second time, that's the gold," Fox senior said of the last gate.

"I'm proud - she was in the race - she made mistakes, she came back and was still in the race right down to the wire and comes away with a bronze, but what a fight."

At the past two Games, and particularly Rio where she was also favourite, Fox had to stew on her result until the next Olympics.

But this time she will also line up in her favoured C1 with the women's event introduced to the Olympic schedule for the first time.

A four-time C1 world champion, Fox fought to get the canoe race included to give female paddler's equality at the Olympics.

"It is exciting to be able to race in C1 - I'll clean my mind, do my race analysis for C1 and come back fresh.

"It's not so much about a second chance, it's stand-alone for me.

"It's a historic moment for all of the women and it's special to be a part of it."

Australian Associated Press