The holding midfielder, nicknamed the 'brain' by Germany coach Joachim Loew for his ability to orchestrate the team's quick passing game, did not train with the squad on the first full day of a training camp in the Italian Alps.
He is only gradually returning to full fitness following a knee inflammation which caused him to miss Bayern Munich's German Cup final win over Borussia Dortmund on Saturday, the latest in a succession of injuries this season.
"He has his programme and we have to see how he handles it," Flick told a news conference in northern Italy.
Schweinsteiger, key for Germany's flowing attacking game, is not the only injury concern with top striker Miroslav Klose also undergoing individual training to catch up after missing much of the season.
First-choice keeper Manuel Neuer and captain Philipp Lahm are expected to join their teammates on Friday after undergoing intensive treatment in Munich for injuries picked up in the Cup final.
Neuer, who is wearing a sling following a shoulder injury, is expected to be fit for the tournament starting in June, although officials have put new Barcelona keeper Marc-Andre ter Stegen on standby.
"Manuel was treated for six hours yesterday," Flick said. "Marc has been informed. (goalkeeper coach) Andreas Koepke phoned him and told him not to leave on holidays.
"But we all expect Manuel to be fully fit and play. We should not discuss too much about it. Manuel is the keeper we want at the World Cup."
Dortmund's Roman Weidenfeller and Hanover 96's Ron-Robert Zieler were the other two goalkeepers selected in Germany's provisional squad.
Germany play Cameroon and Armenia in friendlies before leaving for Brazil where they face Portugal, Ghana and the United States in Group G.