Mickey Mouse Hits Back At CarTOON Joe!
The 62-year-old admitted a charge of improper conduct after launching an attack on Atkinson's performance in the 2-1 defeat at Fulham on November 9.
However, a charge of using abusive and insulting words towards a match official during his side's 2-2 home draw with Stoke on December 6 was found "not proved".
An FA statement: "At a regulatory commission hearing today, Newcastle United manager Joe Kinnear was fined £500 and warned as to his future conduct.
"Kinnear admitted a charge of improper conduct relating to media comments made about referee Martin Atkinson after Newcastle's match against Fulham on November 9.
"Kinnear denied a further charge of using abusive and insulting words towards a match official relating to Newcastle's match against Stoke City on December 6.
"Kinnear was sent to the stands during this match after contesting the award of a free-kick. The commission found this charge not proved."
Kinnear is facing a further charge of improper conduct after clashing with Hull boss Phil Brown on the touchline during his side's 1-0 FA Cup third-round replay defeat at St James' Park on January 14.
Kinnear has until February 3 to respond to the outstanding charge.