The 41-year-old, who also won the world title in Daegu in 2011, came out of a two-year retirement to make his bid but failed to meet the qualifying mark of 77 metres while finishing 12th at the Japan national championships.
"The result was 64 meters but it came from me giving my best. My preparation period was short but I also feel (I have reached) my physical limit," Murofushi told the Kyodo news agency.
"I feel it was good to compete in these championships again after a while out but I'd like to wish my best for the fellow throwers from now on.
"I think my physical limitations will make it difficult for me to aim for the very top, like winning medals in the Olympics and the world championships.
"I'll keep training on a daily basis but I think it's at different level to aiming for the top and the Olympics."
Murofushi, who had been seeking a 21st national title, also finished ninth at his first Olympics in Sydney in 2000 and fifth in Beijing in 2008.
(Reporting by Nick Mulvenney in Sydney; Editing by John O'Brien)
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