Police arrested the man on a knife possession charge after finding a bloodstained knife in the back of his car, a police spokesman said on condition of anonymity, citing department policy. It was not clear why the man was not arrested in the killing.
Investigators were questioning him in connection with the couple's stabbing and an attack on the wife of another retired bureaucrat earlier this week, a metropolitan police official said on condition of anonymity, also citing department policy.
Investigators also began searching his apartment in Saitama City, north of Tokyo, police said.
Authorities have said they suspected the attacks were connected to the ministry's mishandling of millions of pension records -- a debacle that has drawn intense ire from the public, many of whom lost their retirement funds as a result.
The two officials were retired vice health ministers who were key figures in setting up the pension system 20 years ago.
Kyodo News agency, however, reported that the man told police that he killed the official because of his anger over the death of his pet, for which he held a health official responsible. Kyodo said police also found blood-smeared sneakers, gloves and cardboard boxes in the man's car.
Takehiko Yamaguchi, 66, and his wife Michiko, 61, were found dead Tuesday near the doorway of their home just outside Tokyo.
Hours later, the 72-year-old wife of another former vice health minister was stabbed at their Tokyo home by a man disguised as a delivery man. Yasuko Yoshihara was hospitalized with serious injuries. Her husband, Kenji, was not home.
Koizumi is unemployed and most recently worked as a parcel delivery man, Japanese broadcaster NHK reported.
After the attacks, police beefed up security at the Health Ministry and pension offices, and began guarding current and former top ministry officials.
The government is still scrambling to match most of the 64 million missing pension records with citizens, who paid large portions of their income over many years so they could get stable pension checks after retirement.
Japan has a history of attacks against politicians and officials by extremists.
In 1995, Takaji Kunimatsu, then a police chief, was shot by a gunman suspected of links to a doomsday cult he was investigating. Kunimatsu survived despite serious wounds, but the attacker was never caught. Last year, then-Nagasaki mayor Iccho Ito was fatally shot campaigning for re-election.
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