British Swimming has scrapped funding to Stockport's Intensive Training Centre after its budget was cut.
The governing body had to save £3.7m after a poor showing at London 2012.
Following the 2008 Games in Beijing, ITCs were set up in Bath, Loughborough, Stirling, Swansea and Stockport to help swimmers with training, sports science and medical support.
British Swimming will still fund the other four ITCs and will offer support to the existing Stockport Metro Club.
"Our Olympic performance debrief gave a clear indication that the system underpinning swimming is world class and the ITCs at the heart of that system are clearly important," said British Swimming chief executive David Sparkes.
"However, with significant budget cuts it has been necessary to look across the sport at savings and, while we've achieved considerable cost reductions in a number of areas already, it was inevitable that we should have to focus our more limited resources and operate with fewer ITCs."
Stockport was the former base of Keri-Anne Payne, who won an open water silver medal at the Beijing Olympics in 2008, while Athens bronze medallist Steve Parry and James Hickman were two other Great Britain swimmers to have trained there.
The futures of coach Sean Kelly and Stockport's two full-time swimmers, James Goddard and Russell Smith, are yet to be confirmed.
Of the other four ITCs, the University of Bath and Loughborough University will continue for a further four years on more cost-effective terms, while Stirling and Swansea have been extended until the end of 2013, also on a reduced rate.
New British Swimming national performance director Chris Spice and head coach Bill Furniss will define longer-term strategies.