Seven people, including four working on quake reconstruction, were missing, and calls for rescue were swamping the fire department, public broadcaster NHK reported.
Hourly rainfall hit a record 121mm on Saturday morning (local time) in Wajima, while neighbouring Suzu received 84.5mm in an hour, also an all-time high.
TV footage showed brown floodwater turning streets into rivers in Wajima, with cars half submerged.
Eiichi Higashi, a Wajima resident taking shelter at an evacuation centre within the city, told NHK that people were rushing to the facility as evening neared.
"It's tough to see people who live in temporary housing after losing their houses to the quake now coming to yet another shelter because of the rain," Higashi said.
Military personnel have been dispatched to the region to work on a rescue mission along with police officers and fire fighters, Chief Cabinet Secretary Yoshimasa Hayashi told reporters.
"This is heavy rain in the region that suffered massive damage by the Noto peninsula earthquake. There must be many people who are very worried," Hayashi said.
The 7.6 magnitude quake killed more than 300 people in Suzu, Wajima and surrounding areas.
