The four-time WMX champion was set to line up for the fourth round in Teutschenthal, Germany, but a four day turnaround from her operation put paid to that.
The Dunedin rider, who is based in the Netherlands with her team, F&H Racing, had a small crash on her final day of training last week and landed awkwardly on her knee.
She headed to Belgium on Monday where she had an MRI and then underwent surgery to repair the damage.
"The injury itself is not too significant, but with the next round of the championship this weekend I’ve had to withdraw," Duncan told the Otago Daily Times.
"A four day turnaround just simply doesn’t give the knee enough time to heal, therefore the risk is too high."
Duncan, who sits fifth overall after round three earlier this month, is no stranger to injuries, having been hampered by a broken collarbone in 2022 and spending three months off the bike during preseason for this campaign with a micro fracture in her knee.
"Anytime you get knocked down with an injury it’s disappointing, frustrating and that side of it never really gets easier.
"At the same time I know how it goes, I’ve been here before."
While disappointed, there was "no time to sulk".
She starts physio today and will be throwing everything into it to get back on the bike.
"Who knows, I could be back on the bike in Maggiora in two weeks’ time, but that’s something we will be taking day by day.
"If I’m strong enough I’ll be there. If not, then we won’t force it."