The man was taken into custody outside the farm property near the city of Nakano in Nagano region, with police confirming a fourth fatality overnight — an elderly woman who was found injured at the scene and later pronounced dead.
A police spokesman told AFP that the suspect had been detained at about 4:30 am.
It was a rare instance of violent crime in Japan, which has a low murder rate and some of the world’s toughest gun laws.
The suspect hid for several hours in the house, which belonged to his father — the speaker of the Nakano city assembly, the Kyodo news agency said.
He allegedly stabbed his victims with a large knife, before using a hunting rifle to shoot two policemen who responded to emergency calls.
Authorities had urged people to stay indoors in the semi-rural area of central Japan after the rampage started on Thursday afternoon.
The slain officers were identified as Yoshiki Tamai, 46, and Takuo Ikeuchi, 61.
Two women, including the suspect’s mother, had escaped the house where the suspect was holed up, one at around 8:35 pm and the other soon after midnight.
‘Help me’
A witness told the NHK public broadcaster he had been working at a farm nearby when “a woman came running from the road saying, ‘help me’, and she fell down”.
“Behind her came a man wearing camouflage and carrying a large knife, who stabbed her in the back,” the 72-year-old witness said.
He said he called emergency services while neighbors tried to resuscitate the woman.
NHK, citing police, said the attacker then fired what appeared to be a shotgun at police officers who arrived at the scene.
The officers were inside a patrol car and the attacker placed the weapon against a window of the vehicle and fired twice, NHK reported.
There was no known motive for the attack.
Japan was left reeling in July last year when former prime minister Shinzo Abe was shot dead in broad daylight with an apparently homemade gun.
Abe’s accused assassin, Tetsuya Yamagami, reportedly targeted the politician over his links to the Unification Church.
And last month, a man was arrested for allegedly hurling a pipe bomb-like explosive towards Prime Minister Fumio Kishida as he campaigned in the western city of Wakayama.
Kishida was unharmed and a man arrested on the scene will undergo a three-month psychiatric examination, a regional court said this week.
The suspect has reportedly remained tight-lipped about his motive for that failed attack.