Yeo was handed the new role a day after Chun was placed on leave after officials launched an investigation into the South Korean's training methods following complaints of abuse from athletes.
"Jun has been with US speedskating since 2010 and while he was named in the grievance there have been no specific claims made against him therefore he will coach the team for now," USS spokeswoman Tamara Castellano said.
"The athletes that are currently in the national racing program are comfortable skating under Jun."
Nineteen skaters, including five Olympic medallists, filed a grievance complaint about Chun, claiming verbal, physical and psychological abuse.
The complaints include accusations that he once slammed a skater against a wall and that he repeatedly insulted female skaters by telling them they were "fat" and that he also forced other skaters to train while they were recovering from injuries.
The USS said it hoped to complete the investigation before the start of the short track World Cup team trials on September 27 in Salt Lake City.
The investigation will be conducted by New York law firm White & Case, which is part of the United States Olympic Committee's Safe Training Program.
"Obviously this is not something any national governing body wants to have happen," said Castellano.
"The safety, security and well-being of our athletes are always our prime concerns and we hope we can deal with this as quickly as possible so everyone can move onto training in a safe and comfortable environment as we move closer to Sochi (2014 Winter Olympics)."
Chun, who formally coached the South Korean national team before being recruited by US speedskating in 2007, has denied the accusations.
"I have not abused athletes in any way and am confident I will be found innocent at the outcome of the investigation," he said in a statement.