Video report by ITV News Correspondent Damon Green
Jones was most recently known for playing Sandy Thomas in the soap from 2005 until 2018.
Lesley Duff said: "It is with great sadness that I can confirm the death of Freddie Jones.
"He passed away on the evening of July 9 after a short illness.
"Freddie was a much loved and admired actor, known for his triumphs in classical theatre, film and television. He will be greatly missed by all who had the pleasure of knowing him and most especially his family."
Emmerdale actors Mark Charnock and Charlotte Bellamy pay tribute to 'legend' Freddie Jones
Emmerdale actor Charlotte Bellamy marveled at Mr Jones' energy on set even in his 90s, while Mark Charnock hailed him as "wonderful".
Ms Bellamy said: "He was just a huge inspiration, if I could be working when I'm 90 like he was then it's just incredible."
The father of fellow actor Toby Jones, he became an actor after a mid-life career change, having previously worked as a laboratory assistant while performing in amateur theatre on the side.
His first acting credit was on the TV mini series Androcles And The Lion in 1960 and he worked steadily on the small screen, including as Claudius in the TV miniseries The Caesars.
His big-screen debut was in Marat/Sade in 1967 and he also appeared in literary dramas such as Far From The Madding Crowd and Nicholas Nickleby, as well as the 1987 version of Vanity Fair.
Jones appeared in Hollywood films including The Elephant Man, Dune, Firefox and Wild At Heart.
More recently he played a number of roles in Heartbeat and Casualty before becoming a regular on Emmerdale in 2006.
He announced his departure from the soap in 2018, saying he could not justify staying, even though he had been offered another year on the show
Film producer Jonathan Sothcott paid tribute to Jones, tweeting: "Freddie Jones has died. One of Britain's great character actors. Remarkable in The Elephant Man, The Man Who Haunted Himself, Young Sherlock Holmes & so, so much more. One of @hammerfilms best monsters in Frankenstein Must Be Destroyed. A remarkable legacy. RIP."