Germany's World Cup winner Goetze has suffered with muscular problems in recent months, prompting a comprehensive internal investigation into the possible causes, the club said on Monday.
"Those investigations revealed the player has metabolic disturbances, rendering it absolutely necessary to withdraw him from team training for the time being," said a statement.
The 24-year-old Goetze, who scored the winning goal against Argentina in extra time in the 2014 World Cup final, has featured for only 24 minutes of league action so far this year.
"I'm currently undergoing treatment and will do everything in my power to be back in training and helping my team to achieve our common goals as soon as possible," Goetze said in the statement on the club's website (www.bvb.de).
Dortmund are third in the Bundesliga standings, 13 points adrift of leaders Bayern Munich with 12 matches left. They are also in the Champions League last 16 where they trail Benfica 1-0 from the away leg ahead of the return on March 8.
They visit third-tier giant killers Sportfreunde Lotte in the German Cup quarter-finals on Tuesday.
"We're happy to have now uncovered the reasons for Mario's difficulties and are convinced that his extraordinary abilities will give us additional quality once he has completely recovered from this," said Dortmund's sporting director Michael Zorc.
Goetze has scored just two goals in 16 appearances for Dortmund in all competitions after returning to his hometown club for this season.
It has been a poor return on the 22 million euros ($23m) it cost to buy him back from Bayern, who forced Dortmund to sell him for 37 million euros in 2013 when the Bavarians triggered a release clause in his contract.
Goetze failed to hold down a first-team place at star-studded Bayern in three seasons under Pep Guardiola, who preferred the silky skills of Thiago Alcantara to Goetze's industry around the edge of the box.