Emanuel's comments came Thursday, a day after Jackson's office said he is being treated for an unspecified mood disorder, the Chicago Sun-Times reported.
Jackson's leave has led to questions about why more about his condition has not been made public.
"Just because you're in public life doesn't mean your zone of privacy ends. At some point, he has to talk to the constituency, and he knows that but ..." Emanuel said before being cut off by a question.
Jackson has been on medical leave since June 8.
Emanuel said Jackson's not missing much in Congress.
"I know a lot of people are saying, 'When is he going to get back to work?'" Emanuel said at a Chicago high school where he announced an international baccalaureate program.
"Why should he get back to work to a Congress that does no work? Why rush it? Last time I checked, Congress had their second repeal of the healthcare bill. Why rush? Take care of your health. Guess what: Congress is going to be there. Hopefully, when you return they'll be doing real work."
Mood disorders can include bipolar disorder and depression.