The Intensive Training Centres (ITCs) in Swansea and Stirling will shut after governing body British Swimming’s Olympic budget for Rio 2016 was cut.
UK Sport reduced funding by £4m after Britain’s swimmers failed to reach a target of five medals at London 2012.
Stockport’s ITC shut in February, but bases in Loughborough and Bath, which house more elite swimmers, are safe.
Training facilities will still be available to swimmers in Swansea and Stirling, but without the same level of support as before.
British Swimming has pledged to continue investing in the sport in Wales and Scotland as part of a deal with their respective governing bodies.
The deal with Scottish Swimming and Swim Wales will run from 2014 to 2017.
The closing of the ITCs comes a month after Swansea learned funding for its disability swimming programme was being pulled.