The seasonally adjusted jobless rate fell from 3.0 percent in May, improving for the first time since March, according to the Ministry of Internal Affairs and Communications.
Meanwhile, the Ministry of Health, Labor and Welfare said the job availability ratio increased to 1.13 from 1.09 for the previous month, meaning there were 113 openings for every 100 job seekers.
Japan has lifted the state of emergency, which requests restaurants to close early and citizens to refrain from unnecessary outings, in nine prefectures including Tokyo.
But Tokyo was put under a state of emergency again in mid July until late August due to a resurgence of infections, and four more prefectures are now projected to be added to the measure, which clouds the outlook for the hiring environment.
With unadjusted figures for seasonal factors in the reporting month, the total number of unemployed people rose 110,000 from the previous year to 2.06 million, but those in work also rose 220,000 to 66.92 million, the ministry said.
The sector of accommodation and eateries services, hit hard by the pandemic, recorded the first year-on-year growth in the number of workers in 18 months, up 130,000 from a year earlier to 3.82 million.
The wholesale and retail fields showed a rise of 490,000 from the previous year to 10.71 million, increasing the largest number of jobs among others.