The 31-year-old was fourth at the Games in Delhi in 2010 and was part of Team GB at London 2012.
"The news of this anti-doping rule violation has come as a great shock to me," he said in a statement.
"From the outset, I would like to state that I have not knowingly taken any banned substance."
UK Athletics has confirmed that Warburton has the opportunity to respond to the charges against him and can also have the charges determined at a full hearing before the National Anti-Doping Panel.
"I recognise that the responsibility for this situation lies with me and I'm committed to working with UK Anti-Doping and will fully cooperate in the legal process," Warburton said.
"I'd like to take this opportunity to wish the best to all my team mates heading to the Commonwealth Games and apologise that I won't be able to join them as part of Team Wales."
Team Wales Chef de Mission Brian Davies said: "Team Wales can confirm that one of the competitors selected for the Glasgow 2014 Commonwealth Games has been provisionally suspended after being charged with committing an anti-doping rule violation.
"As a result Gareth Warburton will no longer be able to compete at the Games."
Welsh 800m runner Gareth Warburton is out of the Commonwealth Games in Glasgow after being charged with anti-doping rule violations.