The Welshman competed at the 1992 Paralympics in Barcelona for the shot put and the javelin.
He also won World Championships silver for the shot in 1994 held the world record.
Hughes transitioned into performance management in 1999 after retiring and was a key figure in advancing Welsh inclusive and Para-sport with his role at Disability Sport Wales.
The organisation confirmed he suddenly sadly passed away on December 30.
Disability Sport Wales tweeted: “Ant was a loving father and brother, our Performance Manager, friend, colleague, athlete, coach, and an absolute advocate, champion and ambassador for disability sport in Wales and across the world.
“His reach and impact was unsurpassed.
“His determination to ensure everyone achieved their potential through opportunity and equity was unparalleled, and made a difference to so many hundreds and thousands of lives.
“There are no words to express the loss, sadness and disbelief this news brings. Ant will be missed always, but we will continue to fight for the legacy he so believed in – a Wales where sport has equity at its heart and everyone has the right to achieve their potential.
“Ant taught us all so many lessons, inspired us, and gave us so much knowledge through his story telling, and we will honour him in the days and weeks to come with stories about his life, his impact and his legacy.
“Our thoughts are with his family at this hugely difficult time.”
Disability Sport Wales CEO Fiona Read said Hughes “was ahead of his time” and “we won’t ever see the likes of Ant again in sport“.
Hughes worked with the likes of Aled Sion Davies, Josie Pearson and Hollie Arnold who all won Paralympic gold medals.
Under his guidance, the number of Welsh Paralympians rose from 17 in Sydney 2000 to 38 at London 2012 – with 21 in Tokyo 2020 and 14 medals won.
Hughes was named Sport Wales Coach of the Year in 2011, inducted into the UK Coaching Hall of Fame in 2012 and received his MBE from the Queen for services to sport in 2013.