The affiliate is a separate company which supplies Honda - the car manufacturer is its main UK customer - and employs 1,200 staff in the UK.
Hundreds of these employees work in Swindon next to the manufacturing plant in South Marston.
A spokesman announced on Honda Logistics' Japanese website that Honda’s decision to end production of its cars in Swindon and quit Britain made its own business there unviable, so it too will end production.
North Swindon MP Justin Tomlinson said: "We will be speaking urgently to Honda Logistics and other members of the task force to ensure the workforce are properly supported at this troubling time.
"We will continue to work with local and national agencies to make sure that new employment opportunities are identified at the earliest opportunity."
Honda first announced its decision to close the South Marston plant in February and attempts by politicians, business leaders and unions to convince them to stay, and even the organising of a major strike and March march through Swindon, could not change its mind.
Swindon Borough Council and the town's MPs are working with the manufacturer to support all the workers affected and have now pledged to offer help to those in the logistics firm who will also face redundancy.