The 20-year-old Kyrgios was fined $10,000 earlier on Thursday for an obscene sexual remark he made on the court in Wednesday's second round.
The ATP announced several hours later that it was fining him an additional $2,500 for another comment he made to a ball person during the same match.
“Following a review of video from the match the ATP has also issued an additional fine of $2,500 for unsportsmanlike conduct related to a comment he made to a ball person,” the ATP said in a news release on Thursday night.
“In addition, Kyrgios has been served with a 'notice of investigation' which begins a process to determine if his actions also constitute a violation of the player major offence provisions.”
On-court microphones picked up the Australian's scurrilous sexual remark about Wawrinka's girlfriend during a changeover in their match won by Kyrgios when Wawrinka retired with back pain trailing 4-0 in the third set.
Kyrgios said that the woman had been involved with his close friend Thanasi Kokkinakis. “Sorry to tell you that mate,” Kyrgios is heard to say.
Following a 7-5, 6-3 loss to John Isner on Thursday, Kyrgios said that he personally apologised to Wawrinka at Uniprix Stadium and now wants to put the matter behind him but the ATP seems to have other plans.
The ATP said the probe could result in further sanctions against Kyrgios.
“Obviously he [Wawrinka] saw me in the corridor yesterday,” Kyrgios said after his loss to Isner. “He came up to me, as you know he would. I wasn't surprised.
“I told him I was sorry. Obviously he was angry, so I just had to deal with it. Hopefully we can just put it behind. It's all cleared now. I apologised in public and privately as well.”
Writing his public apology on Facebook, Kyrios said: “I would like to take this opportunity to apologise for the comments I made during the match last night v Stan Wawrinka.”
“My comments were made in the heat of the moment and were unacceptable on many levels.
“In addition to the private apology I've made, I would like to make a public apology as well. I take full responsibility for my actions and regret what happened.”
An angry Wawrinka had demanded action by tennis authorities over the “beyond belief” comments.
Wawrinka, who separated from his wife earlier this year and has been linked to Croatian tour player Donna Vekic, said the ATP should take “major action this time”.
Kyrgios hopes the incident won't dog him as he now travels to Cincinnati for next week's pre-US Open event.
“I've been fined. So everything is sort of put to bed now. I thought we could move on from it,” said the world number 41.
'There's no excuse'
Kyrgios' insult rocked the sport and the criticism has come from all directions, including world number one Novak Djokovic.
Top seed and three-time winner Djokovic racked up his 50th win of 2015 to reach the quarter-finals, scoring his 28th consecutive victory at the Masters level by seeing off Jack Sock of the United States 6-2, 6-1.
The Serb then commented on the Kyrgios incident.
“He was fined, he deserved it,” said Djokovic. “I think he's going to learn a lesson in a hard way.
“I understand that every player goes through certain tantrums, emotional ups and downs during the match. In a big fight and at this level, I understand.
“But… there's no excuse of directing your tantrums to your opponent.”
Second seed Andy Murray, who is chasing a third title in Canada, also took his season's win tally to 50 with a smooth 6-3, 6-2 triumph over Luxembourg's Gilles Muller.
The Scot took a softer line to Kyrgios than Djokovic.
“The most important thing is that he learns from what happened yesterday,” Murray said.
“There's obviously certain things in tennis, in our sport. In other sports that sort of thing happens more often than we imagine, in a lot of team sports especially.
“In tennis there are certain things you shouldn't do. That was probably one of them.”
Added Rafael Nadal: “It's obvious that when you are in the tour, you are in the locker room every single week of the year, you are with colleagues around, and the life is much easier and more happier if you have a good relationship with the rest of the players.
“What happened yesterday doesn't help to do that.”