Police in the German capital said on Twitter that all buildings in an 800-meter (875-yard) radius around the site will have to be evacuated on Friday morning as a precaution, AP reported.
The central station, a major hub for long-distance trains, is just inside that area. It also includes a hospital run by the German military.
It wasn't immediately clear on Wednesday what impact the operation will have on train services.
More than 70 years after the end of the war, it is still common for unexploded bombs to be found during construction work in Germany, often requiring temporary evacuations.