The gunman was apparently a Kosovo national, he said.
Security round the airport has been tightened and an investigation is under way, Rhein said.
“Whether the incident was linked to terrorism I cannot say at this stage,” he told journalists.
A spokesman for Frankfurt airport operator Fraport said the shooting took place in a U.S. Army bus in front of Terminal 2.
Chancellor Angela Merkel, speaking in Berlin, confirmed the deaths.
“We don’t know the details but I would like to express how upset I am. We have to do everything we can to find out what happened,” she told a joint news conference with Portuguese Prime Minister Jose Socrates.
The U.S. Army and Air Force and German police at the airport were not immediately available for comment.