In August, the index, which surveys workers such as taxi drivers, barbers and hotel and restaurant staff, fell to 41.7, the first drop recorded in eight months.
September’s rise beat the 21-month high of 42.4 recorded in July.
The output index, which records the level of confidence in future conditions, rose to 44.5 in September from 44.0 in August.
Also released today, the Bank of Japan’s preliminary balance of payments statistics showed that Japan’s current account surplus rose 10.4% to ¥1.712 trillion (£12.06 billion) over the year to August.
However, Japan’s trade surplus fell to ¥304 billion in August, from ¥437 billion in July.
Exports fell 7% over the month to ¥4.23 trillion, a 37.1% fall year-on-year.
Imports were ¥3.92 trillion in August, a 5% fall from July and 42.8% year-on-year fall.