Williams, 30, who won gold at the 2012 European Championships and bronze at the Delhi Commonwealth Games in 2010, and was co-captain of the Wales squad In Glasgow, said he was "utterly devastated" at the news.
"UK Anti-Doping can confirm the provisional suspension of athlete Rhys Williams after being charged with committing an anti-doping rule violation under the IAAF Anti-Doping Rules," UKAD chief executive Andy Parkinsonsaid in a statement in response to an announcement by Team Wales.
"The athlete has the opportunity to respond to the charges against him, and to have those charges determined at a full hearing before the National Anti-Doping Panel.
"UK Anti-Doping will not be making any further comment."
Williams, the son of former Wales and British and Irish Lions rugby winger JJ Williams, failed an in-competition test at the Glasgow Grand Prix event on July 11 and has been given a mandatory provisional suspension from all competition.
He said he had not knowingly taken a banned substance.
"I am utterly devastated about the news of this anti-doping rule violation, which has come as a great shock to me," Williams said in a statement.
"From the outset, I would strongly like to state that I have not knowingly taken any banned substance.
"As a professional athlete, I have always supported and have been an advocate of clean sport."
Williams said he would fully co-operate with UKAD.
"To be named Co-Team Captain for the Welsh Athletics Team was a great honour and I am distraught that I won't be able to fulfil this role and join them as part of Team Wales.
Welsh 800m runner Gareth Warburton was provisionally suspended this month for an anti-doping violation, ruling him out of the Games.
Welsh Olympic silver medal-winning boxer Fred Evans had his accreditation refused after an investigation by theHome Office and Games officials.