Jones, who initially joined the club as a physio but then took over the first team coach role after the departure of Richard Hill, leaves the club with immediate effect.
Gills chairman Paul Scally said the move was the first in a number of changes that are going to be made in the coming weeks.
Talking to BBC Radio Kent, Scally said, ‘It was an extremely hard decision as Wayne’s a lovely man.
‘But clearly changes needed to be made and I intend to make a number of changes in the next week or so.’
Jones was believed to be working without a contract, so the move will not have a financial effect on the club, in terms of paying off remaining time on the deal etc.
Clearly something needs to be done at Priestfield to halt the poor run of results – and Scally has reportedly suggested that he is in the market for an experienced head to work alongside manager Andy Hessenthaler, whose job is safe.
As someone who met Wayne Jones at the Blues Rock Café last season, I can completely agree with Scally in that Wayne is a lovely guy. He was an affable chap, who was all too happy to come up to myself and my girlfriend and have a chat. It’s sad that he has to move on, but there is a real need for some freshness at the club. We at Gills365 thank him for his service to the club and wish him well for the future.