No problems were anticipated but the player is now back in Brazil after a late hitch.
A Flamengo director said: "We expect him at Ninho do Urubu this afternoon (to start pre-season). We had agreed to sell him for a fee, he arrived in London, Arsenal changed (the terms). Flamengo is a serious club."
Arsenal sources say Mari, 26, a former Manchester City centre back, had his medical and was set to sign with friends even congratulating him on his move but negotiations have now stalled at the final stage.