I'm almost certain that it's a lot less. I seem to remember it being c. 1.5 mill - i.e. about 10%. Googling Bevoelkerungsentwicklung Ostdeutschland I got a little over a mill for 1990-2002
http://www.thilolang.de/projekte/sdz/magazin/0401/5mai.htm

A different paper says the total from 1989-2001 is 1.4 million people of net East-West migration. Of that a good half in 1989-1990 with almost 400,000 net migrants each of those two years, explaining the difference between the two papers (first doesn't include 1989). Both have interesting details if you feel like learning more about the topic. (auf deutsch). They confirm that it is primarily young people (twenties, thirties) that leave and also note that after the initial surge women outnumber men almost 2:1 among the migrants.
http://www.berlin-institut.org/pdfs/Kroehnert_Ostdeutschland.pdf