But a spokesman also insisted there would still be a strong contest between the remaining contenders — Budapest, Los Angeles, Paris and Rome.
The terror attacks in Paris and worries about the cost of hosting the 2024 Olympics were blamed by organizers for the rejection by 51.6 percent of Hamburg voters of bidding for the event. Polls in September had shown a large majority in favour.
"Having followed the discussions in Germany over the last weeks, this result does not come as a complete surprise," said an IOC spokesman.
"With this decision a great opportunity for the city, the country and the sport in Germany is lost."
The spokesman said Hamburg would miss about $1.7 billion (1.6 billion euros) in IOC investment while the city had estimated it would need 1.2
"It is understandable that the citizens of Hamburg are very sensitive with regard to the not yet finalized financing plan of the candidature. Even more so in a situation in which Germany has to manage a historic challenge with a high number of refugees coming into the country."
It is the second time in two years that a German city has voted against an Olympic bid however.
In 2013, Munich, the last German city to host the Games in 1972, rejected a bid for the 2022 Winter Games.
More worryingly for the IOC, the Norwegian capital, Oslo, and Sweden's Stockholm withdrew from the 2022 race because of the lack of political support amid cost worries.
The Polish city of Krakow pulled out after a referendum defeat.
The Ukrainian city of Lviv backed out because of the country's conflict with Russian-backed rebels.
And before Hamburg, the US city of Boston also got cold feet amid political wrangling over the cost.
"I do not think the 'no' vote from Hamburg was a failure for the IOC, but I do think it reflects the current concerns the general public has about the
risks involved in hosting mega events," said Patrick Nally, a top sports marketing specialist.
The IOC has already reformed its bidding rules to make them cheaper and less bureaucratic.
But Nally said more needs to be done.
"I fear that if Paris and Rome were pushed to do referendums, it is highly likely similar results (to Hamburg) would be found.
"Currently Europe is not feeling very optimistic and this will, I think, create a negative result to any Olympic referendum currently in the European
Despite Hamburg's rejection, the IOC spokesman said: "Now there will be a strong competition with four excellent candidate cities, Budapest, Los Angeles, Paris and Rome for the Olympic Games 2024."
A decision will be made in mid-2017.