They accused the County Government of imposing tough regulations without consulting them.
The association’s chairman Obedi Muruli said members were willing to consult with the authorities to find solutions to traffic jams.
“We want consultations in relation to the new rules; they are now killing the transport industry,” he complained.
According to the County Government, Tuk Tuks will no longer be allowed to operate on Digo and Nkrumah roads as well as Moi, Jomo Kenyatta, Nyerere and Nkrumah avenues.
The three-wheeled motorised vehicles are popular in the coastal town as they are cheaper than ordinary taxis.
Mombasa County’s Transport and Infrastructure Executive Mohamed Abbas said the new rule will take effect on September 1.
Operators are however free to move around Old Town, Kizingo, Makadara, Ganjoni, Mombasa Hospital, Blue Room, Railway, Pandya Hospital, Uhuru na Kazi and Majengo.
The Tuk Tuks are also to be branded with different colours; green (Island), blue (Nyali), red (Changamwe) and yellow (Likoni).