Numbers have fallen by 6% since last year, said the Steam Packet Company.
Figures show 13,228 motorbikes and 35,500 passengers travelled to the 2016 race festival, compared with 14,055 and 36,000 respectively in 2015.
A spokesman said the downturn was "anticipated" because a fast craft, normally used to carry fans from Northern Ireland, was unavailable.
Steam Packet Chief Mark Woodward said: "Suitable vessels for the ports we serve are simply not available for short-term charter, so we had anticipated this situation and taken steps to mitigate the impact.
"Substantial investment in a removable mezzanine deck for Manannan created additional capacity to carry more motorcycles.
"Extra room for visitors and their vehicles was also made available on Ben-my-Chree thanks to the charter of MV Arrow, which took over freight duties".
The Steam Packet company said reservations for next year indicate "strong interest" with 3,500 bookings made already for 2017.
Fewer tourists by ferry travelled to this year's TT races  because a vessel was unavailable, its operator said.