Koizumi's remarks were made Monday before the 50th anniversary of the recognition of what is known as Minamata disease.
It's named after the area in Kumamoto Prefecture in southern Japan where chemical maker Chisso Corp. dumped tons of mercury-laden wastewater into the sea. In the 1950s hundreds of residents died, thousands were disabled and there were innumerable birth defects.
"The issue of Minamata disease that occurred in the course of Japan's rapid economic growth not only caused serious health hazards, but also inflicted a heavy sacrifice on local communities," Koizumi said, Kyodo News reported Friday.
"On behalf of the government, we feel keen responsibility and frankly apologize for the failures to take appropriate steps for a long period and to prevent the spread of sufferings from Minamata disease," he said.
May 1, 1956, is the day the disease was brought to light for the first time and the first official apology came from the Supreme Court ruling in October 2004 that held the state responsible.