Half of the 242 seats in the chamber are being contested.
Polls show Shinzo Abe’s Liberal Democratic Party (LDP) and its allies could secure a majority, meaning a ruling party would control both houses of parliament for the first time in six years.
The deadlock in parliament has been seen as a key factor in Japan’s recent “revolving door” of prime ministers.
Polling stations opened at 07:00 and will close at 20:00.
Despite the importance of the election, early turnout was a little down from the last upper house poll in 2010.
Japan’s upper chamber, while not as powerful as its lower house, is able to block legislation introduced by the government.
No single party has a majority, although the opposition Democratic Party of Japan has the highest number of seats.
Opposition parties have had enough combined seats to control the upper chamber in recent years, leading to what has become known as a “twisted parliament”.
This has resulted in factionalism and multiple changes of prime minister.
“We need political stability to carry out policies,” Shinzo Abe said ahead of the vote.
“We will get that political stability by winning the upper house election.”
Shinzo Abe has relatively strong public support for his proposals for economic reform known as “Abenomics”, which seek to revive the economy, stagnant for two decades.
“I want them to carry on doing their best as the economy seems to be picking up,” one voter, Naohisa Hayashi, 35, told the Associated Press.
“I want to see a stable government. That’s the LiberalDemocratic Party,” 76-year-old Hiroshi Miyamoto was quoted by Reuters news agency as saying, after voting in the western Tokyo suburb of Hachioji.
But other policy changes that Shinzo Abe is seen as likely to endorse may prove to be controversial.
One is restarting Japan’s nuclear reactors – something many in Japan are opposed to.
Another are nationalistic policies that may cause tension with neighboring countries.
This includes the possible revision of Japan’s pacifist constitution, especially a section which prohibits the use of force in international disputes except for self-defense.
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