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The tempestuous Kyrgios had just been beaten in a tiebreak against Johnson when he walked to the net, offered his hand to the American and stormed off court to the bemusement of his opponent and chair umpire Fergus Murphy.
Kyrgios (22) was booed off court by the crowd.
The ATP said on Wednesday (local time) that Kyrgios had been punished for "unsportsmanlike conduct", saying he had failed to complete a medical visit to explain his actions.
Kyrgios, ranked 21 in the world, said later on Twitter that he had been suffering with a stomach bug and a shoulder problem.
"I've been battling a stomach bug for the past 24 hours and I tried to be ready but I was really struggling on the court today which I think was pretty evident from the first point," Kyrgios said.
"My shoulder started to hurt in the practice which didn't help either and once I lost the first set I was just not strong enough to continue. I've not eaten much in the past 24 hours."
Last year, Kyrgios was fined $US16,500 and banned for eight weeks for deliberately throwing a game during his second-round defeat by Mischa Zverev in Shanghai.
The ban for "conduct contrary to the integrity of the game" was reduced to three weeks after he agreed to a "care plan" under the direction of a sports psychologist.
He was also docked a penalty point against world number one Rafael Nadal in the China Open final last week following a disagreement with the chair umpire.