Britain's number one was playing in a quarter-final match against Elina Svitolina, and had gone a set up looking to be in fine form, before her opponent took the second on a tie-break.
The 26-year-old continued into the deciding set, but was forced to retire, down by 3-2, following trouble with her right hip.
Sasnovich shocks Sevastova to book place in final with Svitolina
Svitolina will face either Karolina Pliskova or Kaia Kanepi in the semi-finals of the tournament.
Speaking after the match Konta said: "I don't feel too comfortable saying really too much because, actually, I don't know yet until tomorrow morning.
"Hopefully it's nothing more than a low-grade strain and more muscle spasm more than anything."
With less than two weeks until the start of the Australian Open, the injury will lead to concern over her fitness for the first Gran Slam of the year - one in which she has seen relative success in the last couple of years.
In 2016, Konta progressed to the semi-finals of the tournament, while last year she made it to the quarters before being knocked out by eventual champion, Serena Williams.
The news comes as Andy Murray announced on Thursday he would not play at the Australian Open due to his ongoing hip injury.
"Sadly I won't be playing in Melbourne this year, as I am not yet ready to compete," Murray said.
I'll be flying home shortly to assess all the options but I appreciate all the messages of support and I hope to be back playing soon.
Australian Open tournament director Craig Tiley said: "We are fully aware that Andy has been going through a difficult period with his hip and that he's done everything possible to prepare for the Australian summer.
"Personally, I also know that Andy loves tennis and would do anything to play. This is a very hard decision for Andy and we totally respect it."
Svitolina to take on reigning champ Pliskova in Brisbane semis
Dominant Svitolina cruises into Brisbane quarter-finals