But US defence officials said Gates would give assurances of Washington's "full-throated commitment" to continue to defend its allies in the region.
For his part Yukio Hatoyama, Japan's new prime minister, has taken a more independent-minded stance than his predecessors, recently announcing the Japanese navy would end its refuelling mission in the Indian Ocean in support of the US-led war in Afghanistan.
He has also called for flexibility in handling the controversial relocation of a US military base on the southern Japanese island of Okinawa, and a review of the 2006 agreement with the US.
"It is important for both of us to be flexible," said Hatoyama, hinting at a possible compromise over the relocation.
Japan and the United States agreed in 2006 to move the Futenma air base from an urban to a coastal area on Okinawa by 2014, but Hatoyama has recently said he wants the base off the island, and possibly even out of the country.
The US military presence has long angered Okinawa residents, who say they are fed up with aircraft noise, the risk of accidents and crimes committed by US service personnel stationed there.
Okinawa, the site of one of the bloodiest battles of World War II, hosts more than half of the 47,000 American troops stationed in Japan and has been an important strategic US base for six decades.
The renewed debate over where to move the Futenma base, now located in a densely-populated urban area, has cast a cloud over a scheduled visit to Tokyo by Barack Obama, the US president, in mid-November.
According to Japanese media reports, the US has said it would be agreeable to minor adjustments to the relocation plan such as building runways further offshore, but has ruled out the option of leaving Okinawa.
|Around 47,000 US troops and personnel are based in Japan [EPA]
Defence officials travelling with Gates have warned that any move to review the arrangement could undermine broader and long-standing security arrangements between the two countries.
"It's been in the works for 15 years. It's highly complex and complicated," an unnamed official told reporters ahead of the defence secretary's visit.
"You start to pull on one thread, and you run the risk of the whole thing unravelling."
Another defence official, also speaking on condition of anonymity, told reporters that the accord was "not just a matter of moving troops in barracks but a strategic realignment of US and Japanese forces".
Japan's refusal to honour the terms of the agreement, the official added, would "be a blow to confidence on both sides".