At the start of October Lee was told that he will face no criminal proceedings over allegations of match fixing dating back to 2010.
But after fresh allegations were made of suspicious betting patterns in a match against John Higgins on Thursday, world number seven Lee has been suspended.
"The WPBSA have concluded that it would not be appropriate for Stephen Lee to continue to compete on the World Snooker Tour whilst these investigations are undertaken," World Snooker said in a statement.
"Therefore WPBSA Chairman Jason Ferguson has taken the decision to suspend Stephen from competition whilst this enquiry is ongoing."
In the match in question - a snooker Premier League match - Higgins twice came from behind against Lee to win 4-2.
The Scot was 1-0 and 2-1 down but he took the final three frames, thanks in part to Lee missing a pink and black combination that would have levelled the clash at 3-3.
The WPBSA statement added that they, "have carefully considered both the initial information from the Gambling Commission which was reviewed on 5th October 2012 and the new information regarding suspicious betting patterns in relation to the match between Stephen Lee and John Higgins from 11 October 2012."
Lee's suspension will remain in force until the conclusion of the investigation or any resultant hearings.