The move came a day after Italian police confiscated unidentified substances in a raid on the hotel where the trio was staying in the northeastern town of Lignano Sabbiadoro after the athletes tested positive for banned stimulants.
The trainer is Christopher Xuereb of Toronto.
Udine prosecutors believe the trio violated Article 9 of the doping laws, which calls for punishment for whoever administers or consumes banned substances.
Police were still analyzing the substances seized to determine if they were legal or not.
Being formally placed under investigation is a step up in the Italian justice system from someone simply "informed of the facts," which is how someone can be questioned by police. That occurred after the raid early Monday, when the trio was brought to a local police station.
Police told The Associated Press that the raids were executed following a tip from the World Anti-Doping Agency. Paul Doyle, the agent for the two sprinters, said they worked in conjunction with WADA on the raid after becoming suspicious that Xuereb, their newly hired trainer, might have given them supplements laced with a banned substance. Doyle also said that Powell and Simpson were aware of the impending raid, but Xuereb was kept out of the loop.
"Asafa and Sherone have been tested more than 100 times each through their career ... and never turned in a positive test," Doyle told The AP in a phone interview. "Now they change their supplements and the first time they get tested, they have a positive test? It has to be something in those new supplements that has caused it. Chris is the one that provided those.
"We're not trying to throw Chris under the bus and blame him for anything. We know it has to be something in the supplements he gave them. We're not saying he did anything deliberate, but it's in those supplements. We need to figure out what it was that caused this and from there move forward."
In a statement issued by Xuereb, the Canadian trainer said he's disappointed with Doyle's remarks.
"It is time the athletes took responsibility for their doping instead of looking around for a scapegoat," Xuereb said. "Athletes keep using the same story which is to blame the scapegoat for their own wrongdoing.
"I am extremely disappointed that these athletes have chosen to blame me for their own violations. WADA (the World Anti-Doping Agency) and the public needs to stop accepting these stories and hold these athletes accountable."
Xuereb says he began working with Powell and Simpson in May to "help manage the general health of these athletes," and denied giving either sprinter any illegal substances.
"While I did recommend vitamins, all vitamins recommended by me were all purchased over the counter at reputable Nutritional stores and were major brands," Xuereb said. "I was instructed by the agent and athletes to buy these vitamins ... Although I suggested certain vitamins to these athletes it is ultimately the athlete's responsibility to accept or reject my suggestion."
Xuereb also said that the vitamins he provided to the athletes did not contain any substance found in their positive drug tests and that he has co-operated fully with the Italian police.
WADA director general David Howman likened this case to the doping scandal involving the Austrian cross country skiing and biathlon teams at the 2006 Turin Olympics, when Italian police raided athletes' residences following a tip from WADA and the IOC.
"There's nothing new in relation to the way we operate," Howman added.
Doyle said Tuesday the athletes had left Lignano but declined to say where they went. A hotel receptionist said late Monday that Xuereb had checked out.
Powell and Simpson tested positive for the stimulant oxilofrine at the Jamaican championships last month, Doyle announced Sunday, and the agent welcomed the investigation.
"That must mean they found something. That's good," Doyle said. "The whole purpose of the raid was to see what products there were there and hopefully find whatever it was that caused this positive test. Asafa and Sherone were under the assumption and led to believe everything they were taking was completely legal."
However, Doyle acknowledged that he and the athletes should have been more responsible about what supplements they used.
"In hindsight, we should've been given a list, made sure we got a list," Doyle said. "The extent of what I did, I said to (Xuereb) in a text message, that all supplements have to be cleared by me first. He never cleared them with me. He did send them in an invoice that had the names of supplements in there that he had purchased. But that was it. I didn't have the ingredient list.
"Just looked at it this morning, 19 different supplements (Powell) was given."
Tara Playfair-Scott, Powell's publicist, said in a statement that the runner handed over to police one bottle of Aleve containing 50 capsules and one bottle of 5-hour Energy, berry flavoured.
Doyle added that the athletes would ask for a backup 'B' sample to be tested.
Jamaican athletes have made Lignano their in-season training base for years.
A local athletics meet was scheduled for later Tuesday in Lignano and Jamaicans had been scheduled to compete as they do most years. However, neither Powell nor Simpson was on start lists released Monday.
The news of the positive tests for Powell and Simpson came the same day that American 100-metre record holder Tyson Gay revealed that he also failed a doping test.
Also Monday, discus thrower Allison Randall acknowledged that she was one of the five Jamaican athletes who tested positive for a banned substance at the Jamaican championships last month, along with Powell and Simpson.
Randall holds the island's record for the discus throw and competed at the London Olympics. Her statement says she was "shocked and surprised" at the findings and hopes her backup sample will clear her name.
The Jamaica Athletics Administrative Association issued a brief statement Monday saying an anti-doping management process has started for the athletes. It did not identify the two other athletes who tested positive.
Powell was the last man to hold the 100-metre world record before Usain Bolt broke it in 2008. He also helped the Jamaicans to the 4x100-metre relay gold medal at the 2008 Olympics.
Simpson won Olympic gold in the women's 4x100 relay in 2004 and silver in 2012, along with an individual silver in the 100 in 2008.
The findings come a month after another Jamaican Olympic champion, Veronica Campbell-Brown, tested positive for a banned diuretic.
AP Sports Writers Pat Graham in Denver and Stephen Wilson in London and reports from The Canadian Press contributed.