The 38-year-old from Wiltshire, who has been ranked as high as fifth in the world and began this season at number eight, is alleged to have breached WPBSA rules in matches at four tournaments, including the 2009 World Championship.
The WPBSA said in a statement today it had considered a "large amount of material" before deciding to take action against a player who has been suspended from the sport since October 12.
"The case will be heard at a formal independent hearing arranged by Sport Resolutions UK at a date to be arranged," the WPBSA said.
In a statement, snooker's regulatory body said: "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."
Lee appealed against his initial suspension but that was rejected on October 24 and it remains in force.
The WPBSA statement added: "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."
The rules that Lee will face a hearing over relate to betting, specifically providing information that "is not publicly available" and deliberately influencing "the outcome or conduct of a game or frame".
Lee lost three of four group-stage matches at the 2008 Malta Cup.
He beat Stephen Hendry in the first round and Mark King in round two at the UK Championship later in the year before losing to Shaun Murphy in the quarter-finals.
He lost 5-1 to Mark Selby in the first round of the 2009 China Open, and 10-4 to Ryan Day in his opener at the Crucible.
Lee's career took off in the mid 1990s, as he emerged at a similar time to the likes of Ronnie O'Sullivan, John Higgins and Mark Williams.
He considered quitting when a first-round defeat at the 2008 World Championship saw him fall out of the elite top 16, but played on and after initially struggling to regain form he battled his way back up the rankings and reclaimed a top-10 place.
He has won five ranking titles: the 1998 Grand Prix, 2002 LG Cup, 2002 Scottish Open, 2006 Welsh Open and 2012 Players Tour Championship.
West Midlands Police said in October last year they and the Gambling Commission had ended an investigation into Lee, who was arrested in February 2010 but never charged over match-fixing.
Higgins was banned for six months in 2010 for minor breaches of WPBSA rules after a News of the World 'sting' but match-fixing charges against the Scot were withdrawn.
Barry Hearn, chairman and controller of World Snooker, the sport's commercial arm, has previously said life bans will be enforced for any player found guilty of match-fixing.
Lee responded through his lawyer, Tony Miles, and maintains his innocence.
A statement said: "Mr Stephen Lee wishes it to be clearly known that he denies all allegations brought against him by the WPBSA.
"He does not accept that he has been involved in any breaches of the rules and regulations and is gravely disappointed that a decision has been taken to bring proceedings against him."
Miles said: "Mr Lee is shocked by the suggestions made against him, he has been a professional snooker player for 20 years and has always sought to up hold the highest standards as required of such a player. He has fully co-operated with the WPBSA in its investigation.
"He continues to be suspended by the WPBSA and the impact of suspension and the allegations upon him and his family is considerable.
"As a hearing is now to take place it would not be appropriate to make any further comment at this stage."