The ATP Tour said it had launched an investigation and Kyrgios, similarly hit with a point penalty in losing the China Open final to Rafael Nadal on Sunday, said he was "gutted" to retire against Johnson.
During the tie-break, Kyrgios was 4-2 ahead but could be heard complaining about fatigue as well as declaring his intention to forfeit if he went a set down.
The tournament has not been kind to the temperamental youngster and he was fined and banned for his actions at the event 12 months ago and there is every chance of a similar sanction this time around.
A member of Kyrgios's coaching team told AFP in Shanghai as the player exited the arena that the world-ranked 21 had injured his shoulder.
Kyrgios subsequently took to Twitter to explain he had been battling a stomach bug over the previous 24 hours, but hoped to resume his doubles campaign alongside Lucas Pouille on Wednesday. "Not happy with some of the decisions the umpire is making regarding controlling the crowd". The Briton got to his feet to win the next point, but a forehand into the net set up match point and Cilic's assured volley sealed a 6-3 7-6 (7-5) success. He was consequently suspended.
"I think he's close to his best level - if not he's even improved", Croft said, as quoted in Express.
"What's happening here?" he asked, before muttering: "Exactly why I shouldn't come here".
Johnson wrapped up the set and Kyrgios decided he had had enough, shaking the hands of his opponent and the umpire - though not looking him in the eye - and packing his bag and leaving.
"I'm just going to plan well, just going to try to have a strong finish to the season and see what happens, but clearly I'm aware it's highly unlikely at this point".