The Chinese city was scheduled to host the Asia/Oceania qualifier from 3-14 February.
But the Local Organising Committee announced on Wednesday (22 January) that they had called off the competition after nine people had been killed by the outbreak which is believed to have started in Wuhan.
The event has now been rescheduled to Amman, the capital of Jordan, for 3-11 March.
The inaugural Tokyo 2020 qualifying event will now be the Africa qualifier in Dakar, Senegal from 20-29 February.
Qualifying for boxing is being managed by BTF after AIBA was suspended for finance and governance issues last June following recommendations made by the IOC Executive Board.
"The IOC Boxing Task Force noted today's decision of the Local Organising Committee to cancel the Asian/Oceanian Tokyo 2020 boxing qualifying event which was due to take place in Wuhan (CHN) from 3-14 February 2020, amid growing concerns in relation to the coronavirus outbreak reported in the city," the BTF said in a statement.
"The Task Force continues to work closely with the Chinese Olympic Committee (COC) and all partners to explore alternatives and will immediately National Olympic Committees, National Federations and officials on any development."
Wuhan under lockdown after virus outbreak
The cancellation came hours after Wuhan mayor Zhou Xianwang requested visitors avoid the city and that residents stay put to try and contain the virus.
Major Chinese New Year events, planned for Friday, have also been scrapped.
The coronavirus is a respiratory virus which has infected over 400 and been found in Thailand, Japan, South Korea, Taiwan, and the United States.
Wuhan is a major travel hub with a population of 11 million meaning it could have been spread widely before the first deaths were reported.
It is not thought to be as dangerous as the SARS epidemic early this century with most of the deaths from coronavirus being the elderly or those with pre-existing health conditions.
The IOC’s global Olympic Channel will be the exclusive worldwide digital rightsholder for Boxing Qualification Events for Tokyo 2020. Coverage will include live streaming of all women’s and men’s bouts across all weight categories from the first day of competition through the finals for each of the four Continental Events and the final World Qualification Event. Live streaming coverage _will be available in all territories worldwide at olympicchannel.com and Olympic Channel apps._