Midfielder Leon Goretzka and captain Manuel Neuer have been ruled out of the Nations League games against Hungary and England after testing positive.
Those results followed their visit, as members of the Bayern Munich squad, to Oktoberfest celebrations last weekend.
It is unclear whether that was where the players caught the coronavirus, but social occasions give Flick cause for concern, albeit he is adamant that "life should also go on".
The Qatar 2022 World Cup is coming up in November and December, and Flick wants everyone available.
"This can also affect us in Qatar," said Flick. "We have to react to it and deal with the situation as best we can.
"It's not quite as easy as [saying] you should behave. We in the coaching team are also on the road a lot. Such cases are always annoying, but it's also become a normal situation.
"With a normal flu you also miss out. Covid is of course a bit more aggressive. Of course you have to reduce your contacts a little before the World Cup and consider, should I go there or not.
"You're on the road a lot. Life should also go on. We have to see that we keep it under control. But a certain normality with common sense, I think, is the right way."
Germany plays Hungary on Friday and England on Tuesday (AEST), and Barcelona's Marc-Andre ter Stegen will get a chance to impress in the Hungary game in the absence of Neuer.
"I don't need to keep a secret about the goalkeeper position, Marc will be in goal," Flick said in Thursday's press conference.