Barton has used his Twitter account to strongly criticise the club's hierarchy as a result and he was made to train by himself.
The 28-year-old was also hit with a fine of two weeks' wages and on Thursday only trained with Newcastle's reserves in what has developed into an ugly feud with club officials.
Newcastle FC: "The club and the player have important business to focus on over the coming days and both parties have come to an agreement that we will not comment further at this time.
"We understand the level of interest in the club's decision to offer Joey Barton a free transfer.
"However, it would not be dignified, nor would it serve any useful purpose at this present time, for either the club or Joey to air their private issues on this matter in public.
"The club and the player have important business to focus on over the coming days and both parties have come to an agreement that we will not comment further at this time."