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"I am in the process of getting treatment and I will do everything I can to get back into training as quickly as possible to help my team achieve our common goals," Goetze told the club website yesterday.
The 24-year-old scored in extra-time of the 2014 World Cup final to seal a 1-0 win over Argentina. But this season he has endured a difficult return to Dortmund, struggling with form and injuries, following three unhappy years at Bayern Munich spent mainly on the bench.
It cost Dortmund 22 million euros to buy Goetze back from Bayern, having been forced to sell him in 2013 for 37 million euros when the Bavarians triggered a release clause in his contract.
He has not played at all this month after picking up a leg injury and was dropped for Dortmund's home Bundesliga win over second-placed RB Leipzig at the start of February because of poor form.
The attacking midfielder has scored just two goals in 16 appearances for Dortmund this season. Dortmund, who are third in Germany's top flight, gave no date for his return.
But there is relief that the club now know there is a medical reason for the Germany star's woes.
"We are glad to know the reasons for Mario's complaints and we are convinced that after recovering he will give us extra quality with his exceptional abilities," said Dortmund's director of sports Michael Zorc.
"Mario gets the full backing and maximum support from all of us at Borussia Dortmund on his way back."
Among the games, he will miss is the Champions League round-of-16, second leg clash at home to Benfica on March 8 having lost the first match 1-0 in Portugal.