Mr Lee has faced criticism before for playing golf during times of crisis
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South Korea's Prime Minister Lee Hae-chan has resigned for playing golf when he was supposed to be dealing with a national railway strike.
Mr Lee was criticised by opponents and some newspapers for not overseeing the government response earlier this month.
His resignation, offered to President Roh Moo-hyun on Tuesday, was accepted, South Korea's Yonhap news agency said.
A spokesman for the president said Mr Lee "felt sorry" for the trouble he had caused by acting "indiscreetly".
Mr Lee played the round of golf on a national holiday on 1 March.
But that was also the day when railway workers went out on strike and he was widely criticised for not returning to work.
"Prime Minister Lee said he felt sorry for causing trouble by acting indiscreetly and expressed his intention to resign," presidential spokesman Kim Man-soo told AFP news agency.