Lee, 23, was left in agony following a challenge from Newport midfielder Tom Miller in the first half of Saturday's pre-season friendly and after treatment from paramedics, he was carried off the pitch on a stretcher with his right leg strapped in a brace.
Bolton later confirmed via their official website that the South Korea international had undergone a successful operation after suffering a double fracture - but he looks certain to be sidelined for a minimum nine months.
It is a huge blow for the Trotters, for whom Lee has been a consistent performer since his move to the Reebok in 2009.
Ivan Klasnic scored twice, with a Miller own goal adding to the Trotters' tally. Elliott Buchanan had given Newport the lead before Bolton took control.
Manager Owen Coyle told Bolton's website: "We will make sure Chung-yong gets all the support he needs, as now it is all about his recovery and wellbeing. That is the most important thing.
"The operation went well and we would like to pass on our thanks to the medical staff involved."