The former world record holder was due to take part in the race on May 4, but his manager, Jos Hermens, has revealed he will no longer be able to take part.
"Haile has suffered with a pollen allergy and currently has massive respiratory problems, so he has been unable to train regularly for the last two weeks," he said.
Frank Thaleiser, chief organiser of the Hamburg race, is disappointed that the 41-year-old would not be able to take part but understands his absence.
"Along with 23,000 runners, we had of course wished to see Haile on the start line, but it makes no sense in the current situation," he said.
"We will now strive to look for athletes who were not able to start in London or Boston, but are in good shape and able to add to a strong field."
Gerbselassie, twice Olympic and four-time world champion over 10,000m, broke the world record mark for the marathon in Berlin in 2007, before bettering that 12 months later at the same event.