The ban described as "extreme and unfair," by the Badminton Korea Association will be effective until January 23, 2015, it said in a statement.
The 25-year-old Lee won mixed doubles gold at the 2008 Olympic Games in Beijing and took a bronze medal in the men's doubles in London in 2012.
Lee was expected to compete in the Asian Games in Incheon.
"Their period of ineligibility is from 23 January 2014 to midnight on 23 January 2015, during which time the players cannot participate in any capacity in a competition," the federation said in a statement.
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The Kuala Lumpur-based federation also said that it may impose disciplinary sanction against the Badminton Korea Association (BKA) for failing to keep the BWF informed about the players' movements.
Meanwhile BKA said that the absence of both players during visits by anti-doping inspectors had been due to international competition.
"Lee and Kim did not take any banned drugs, refuse doping tests or intentionally shun them," the BKA said in a statement, describing the ban as "extreme and unfair".