As a result, the Badminton Association of Malaysia (BAM) is placed in an awkward selection position – should they select the two-time Olympic silver medallist ahead of Chong Wei Feng and Zulfadli Zulkiffli.
Lee has only just returned to action following an eight-month suspension for doping which has seen his ranking plummet. After missing out on the start of the current season, the 32-year-old has dropped down to 46th on the latest rankings, behind Chong (32nd) and Zulfadli (41st).
Malaysia are only allowed two entrants per category for the August 10-17 World Championship, and world ranking is generally used to decide which players will represent the country.
BAM may yet select Lee for the event ahead of Chong or Zulfadli, but had hoped that BWF wildcard for their star player would save them from making such a difficult decision, particularly after Lee's long-time rival Lin Dan was given a wildcard for the 2013 event.
"BWF sent us an official letter. They did not say why Chong Wei was not accorded a wildcard except that they are not exercising their right to give a wildcard to any players this year," BAM secretary Ng Chin Chai by The Star on Friday.
"If BWF had given the wildcard to Chong Wei, we would have three qualifiers in men's singles… they have their own reasons."
BAM have until next Thursday to decide which two players to enter into the men's singles draw at the World Championship.