The two-time defending national champion has been battling pain in her lower-right back all season and had scans on the troublesome area on Monday.
Results showed bone damage, and the 21-year-old has been referred to a specialist.
"I am pretty gutted,'' Peeters said.
"But then again, you have got to look at the positives. This year is not really anything too big on the radar for me.
"Rio was obviously there but not a huge focus. If I qualified, it was going to be a pretty long shot. I'm glad it was now and not the year of the Commonwealth Games or something I was a bit more hopeful of qualifying for.''
Peeters, who was named junior sportswoman of the year at the Otago sports awards last May, won the national title the past two years and is the New Zealand record-holder (55.14m).
However, she has not been able to throw pain-free this season and it has shown in her results.
The University of Otago physical education student competed in Canberra earlier this month, but her best attempt was 10m short of her best.
"When you can't throw pain-free and you produce distances like that, for me, that's not acceptable and pretty disappointing,'' she said.
"It's been an ongoing thing since last year, but I just thought it was a tight muscle and it would go away. Unfortunately, it never went away and it actually started to get a little bit worse.''
Peeters had hoped the niggle would not stop her from defending her national title at the Caledonian Ground on March 4-6, but said it was best to address the problem now.
She has not entirely written off competing at the Australian national championships in April, but conceded her season was probably over.
It will depend on what the specialist says later this week, but it is likely she will be reduced to rehab until next season.
"There is damage to the bone there; it's not good with the impact from a javelin throw. I just don't want it to cause anything like a stress fracture, which it could possibly be,'' she said.
"We will wait and see what [the specialist] reckons. It's a pretty hard thing. I don't know anything else but training and a bit of study on the side. Now, the role will be reversed and it will be all go as a student.''
If Peeters is ruled out for the rest of the season, she said she would have a revised training plan, which would include gym work and drills that did not include throwing.
Despite the disappointment of not being able to compete in front of a home crowd in a competition which doubles as an Olympic qualifier, Peeters has vowed to be there to support other Otago athletes.
"I'm pretty determined. I don't like to admit defeat with things like injury. But this is something I just have to accept and try my hardest to work with rehab and get it better so I can come back stronger for next season.''
