"Our alliance with Japan has never been stronger," Carter told reporters while en route to Yokota Air Base near Tokyo.
"This is a two-way street, we provide enhanced security to one another," he added, saying he was "satisfied" with Japan's contributions to the alliance.
Carter met upon landing with US troops, some of the 50,000 stationed in Japan, as part of a two-day visit to the long-time US ally.
He is also due to meet with his Japanese counterpart, Defense Minister Tomomi Inada, and Japanese Prime Minister Shinzo Abe on Tuesday. Abe was the first world leader to meet with Trump after his surprise election victory last month, visiting the president-elect at Trump Tower in New York.
Both men were tight-lipped about what they actually discussed during the meeting, but Abe told the press immediately after that "Mr. Trump is a leader I can have confidence in."
Trump had voiced a skeptical view of the US-Japan relationship during his campaign, questioning the value of the alliance with Japan and saying Tokyo should pay more for the American troops stationed there.
"You know we guard Japan, now if something happens to us Japan doesn't have to help, if somebody attacks Japan we are in World War III, folks, I hate to tell you," Trump said during a March campaign rally in Boca Raton, Florida.
But American officials have pushed back on the notion that Japan is free-riding on the relationship, noting that the Japanese government pays $1.6 billion of the costs associated with basing US personnel there. Some analysts have said that this financial contribution means that it is actually cheaper to keep troops in Japan than it would be to station them in the US.
"Japan reimburses the United States for a large faction of those costs and that's good too ... It shows it's a two-way street," Carter said, adding that having American troops in Japan allowed the US the advantage of being forward-based in the region.
Despite Trump's campaign rhetoric, Pentagon officials are confident that the US-Japan defense relationship will continue.
But some analysts of US-Japan relations are decidedly less bullish.
"Secretary Carter's visit is welcomed to reaffirm the achievements made these several years. But his visit will not reassure Japan as Mr. Trump will not listen to him," Tetsuo Kotani, the senior fellow at the Toyo-based Japan Institute of International Affairs, told CNN
"The US-Japan defense relationship is on solid ground right now, but there are certainly storm clouds on the horizon," Zach Cooper, a Japan chair fellow at the Washington-based Center for Strategic and International Studies, said in an email to CNN.
"Many Japanese are concerned about whether a Trump administration might pursue a policy shift in Asia," Cooper added, noting that while such a dramatic realignment is unlikely, arguments over burden sharing will likely continue to test the relationship.
Officials from both Japan and the US cite recent changes to Japanese law allowing for limited collective self-defense and updates to the US-Japan defense guidelines as symbolic of Tokyo's increased willingness to shoulder responsibility for Japanese and regional security.
The changes sparked protests in Japan and were seen by some as a departure from the pacifist spirit of the country's post-World War II constitution.
New Japanese military roles
Taking advantage of the new flexibility, Japan recently deployed armed peacekeepers to South Sudan, its first deployment of armed military personnel abroad since World War II.
It's the first time the US-Japan defense guidelines have been updated since 1998 and will allow Japanese troops to participate in collective defense outside of the country's territorial waters.
Kotani said that these changes and increased operational flexibility were one way the Japanese government was boosting its commitment to the alliance.
Carter is also expected to discuss the contentious issues surrounding the presence of thousands US Marines on the southern Japanese island of Okinawa.
Efforts are underway to relocate the Marines from Futenma to a new base in a less populated area, but while the relocation is supported by Abe's government, local politicians have undertaken efforts to block the move.
This recalcitrance has caused concerns among American military officials and complicated efforts to reposition US forces in Asia, as part of the administration's "rebalance" to the region.
"We have an obligation to defend Japan and they have an obligation to provide us a place from which to defend them," Adm. Harry Harris, the commander of US forces in the Pacific region, testified before Congress earlier this year.
Threats from North Korea
But perhaps a more immediate concern is the threat posed by North Korea's nuclear and missile programs.
Carter said North Korea's provocations had "catalyzed" increased cooperation between the US, Japan and South Korean militaries.
Harris, who oversees US troops in the region, also cited North ballistic missile launches as cause for concern.
"Pyongyang claims are intended to serve as delivery vehicles for nuclear weapons targeting the United States and our allies, Japan and South Korea ... I must assume their claims are true," he said.
Carter was also due to meet with some of the US forces that are within range of North Korean missiles and would form the line of defense should Pyongyang take any aggressive action in the region.
Carter is also due to tour the Japanese helicopter carrier, the Izumo. Japan has made a concerted effort to boost its military capabilities, particularly in the area of naval and amphibious warfare, with an eye towards both North Korea and an increasingly assertive China.
Both China and Japan claim Senkaku Islands, which China calls the Diaoyus, a series of small islets in the East China Sea. The islands are administered by Tokyo. President Barack Obama, while making no claim as to the islands' sovereignty, has said that they fall under the protections of the US-Japan defense treaty.
Harris said that Obama's declaration had made "a positive effect on the situation in the East China Sea."