The world number 13, winner of last year’s Players Tour Championship finals as well as the 2006 Welsh Open and 2002 Scottish Open, was arrested and bailed on suspicion of cheating in February 2010.
The 38-year-old was then suspended last October following a suspect 4-2 Premier League loss to John Higgins, and the WPBSA have decided to look into the results of his which have come under scrutiny.
The Crown Prosecution Service had decided not to take further action against Lee days prior to the defeat to Higgins.
A WPBSA statement read: “As a result of the referral by the Gambling Commission on 5th October 2012, Nigel Mawer the Chairman of the Disciplinary Committee of the WPBSA, launched an investigation into alleged match fixing by Stephen Lee in relation to matches at the Malta Cup 2008, the UK Championship 2008, the China Open in 2009 and the World Championship 2009.
"The WPBSA has gathered a large amount of material from the Gambling Commission, West Midlands police and third parties in relation to these allegations.
"This has been a complex investigation where the material has had to be traced, recovered and re-evaluated with regard to the WPBSA rules.
"The available evidence has now been considered and in accordance with the Disciplinary Rules, the Chairman of the Disciplinary Committee has decided that there is a case for Stephen Lee to answer in relation to a breach of the WPBSA Members Rules.
"These alleged breaches relate to four matches at the Malta Cup 2008, two matches at the UK Championship 2008, one match at the China Open 2009 and one match at the World Championship 2009.
"The case will be heard at a formal independent hearing arranged by Sport Resolutions UK at a date to be arranged.
"Stephen Lee is currently suspended from competition and Jason Ferguson, the Chairman of the WPBSA, has decided that the suspension will remain in force until the conclusion of the hearing or hearings and the determination of this matter.
"The investigation into the suspicious betting in relation to Stephen Lee’s Premier League match with John Higgins on 11th October 2012 is ongoing."
Snooker has long battled with allegations about their players being involved in match-fixing.
The most high profile incident came in 2010 when then world number one Higgins was handed a back-dated six-month ban and fined £75,000 for breaching rules on discussing betting and failing to report an approach from a party trying to instigate corruption in the game.
Higgins was found not guilty of match fixing.
In 2005 Australian player Quinten Hann was banned for eight years for breaching rules that prevent players from soliciting any payment "in exchange for influencing the outcome of any game".
Last year Joe Jogia was banned from snooker for two years after an investigation into suspicious betting patterns on his snooker shoot-out match with Matthew Selt
Fourteen bets to a total value of £4830 were placed in the Leicester area by two persons known to Jogia on Selt to win the match.
Jogia contacted the two persons placing the bets 77 times and Jogia withdrew from the match, citing injury.
He was banned after failing to explain his contact with two people or the suspicious betting.