"So, even from far away, I can imagine how devastated and discouraged the people of Boston feel about the tragedy of this year's race," he wrote in a piece for the New Yorker magazine titled: "Boston, From One Citizen Of The World Who Calls Himself A Runner."
"Something that should have been pure has been sullied, and I, too -- as a citizen of the world, who calls himself a runner -- have been wounded."
"I've run marathons all over the world, but whenever someone asks me which is my favourite, I never hesitate to answer: the Boston Marathon," he wrote in the article translated from Japanese.
Murakami compared the process of recovering from the scars left by the attack with tackling the Boston Marathon's Heartbreak Hill, a four-mile section near the end of the race.
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"The real pain begins only after you've conquered Heartbreak Hill, run downhill, and arrived at the flat part of the course, in the city streets," he said.
"Only once you've climbed the steep slope and emerged onto level ground do you begin to feel how much you've been hurting up till then. The bombing in Boston may very well have left this kind of long-term mental anguish behind."
Ethnic Chechen brothers Tamerlan Tsarnaev, 26, who was killed in a police shootout, and Dzhokhar, 19, are accused of carrying out the bombing, which killed three and wounded more than 264 at one of the world's premier sporting events.
"Some of the pain goes away over time, but the passage of time also gives rise to new types of pain. You have to sort it all out, organise it, understand it, and accept it. You have to build a new life on top of the pain," he wrote.