Speculation about Lee's position had mounted in recent days, with Paddy Brennan rumoured to be taking over his role at Johnson's County Durham stable.
"After hearing about the approach made by Howard Johnson to Paddy Brennan I was both surprised and shocked," Lee said. "I was also disappointed, especially given all the success that we have had in recent seasons.
"I have always enjoyed a really good relationship with Graham Wylie, and I wish Graham and Howard all the best for the future.
"There will be lots of good horses to ride for Ferdy, but I'll also be chasing mounts up and down the county, and I'll go anywhere to maintain my position in the championship table."
Lee enjoyed a fruitful time with Johnson and Wylie, highlighted by a treble at last year's Cheltenham Festival, where his wins included the World Hurdle on Inglis Drever.
Murphy said he could not believe his luck when Lee became available."We were looking for a top-flight jockey for next season. Events early on in the week forced our hand and it's worked out pretty well for us," the trainer said.
"He's ridden some winners for me in the past. He's very strong, has got a fantastic brain and is totally dedicated."
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