The United States has around 54,000 military personnel in Japan who currently report back to Indo-Pacific Command in Hawaii.
But the countries are planning to upgrade this command structure with a new Japan-based headquarters under an agreement made a year ago between former leaders Joe Biden and Fumio Kishida.
The move is meant to make US and Japanese forces more nimble in response to threats such as a Chinese invasion of Taiwan.
US networks CNN and NBC News reported this week that President Donald Trump's administration could put the brakes on these plans as part of a sweeping government cost-cutting drive.
The reports, which have not been confirmed by Washington, cited a briefing document and a US defence official.
They said a move to halt a planned expansion of US Forces Japan would save around $1.1 billion, but also warned it could create political risk for the US in Japan while reducing the scope of US command and control in the Pacific region.
Japan's top government spokesman Yoshimasa Hayashi said Friday there was "no change" to the countries' agreement to enhance their deterrence capabilities under the US-Japan alliance.
"We want to continue the close discussions between Japan and the United States... to further strengthen the interoperability and responsiveness" of the two militaries, Hayashi told reporters.
He did not comment directly on whether the United States had explained the reported plans to Japan.
Japan is in a multi-year process of increasing its defence spending to the NATO standard of roughly two percent of gross domestic product (GDP).
Now the nation faces a delicate diplomatic dance as Trump presses its allies to take more responsibility, fiscally and otherwise, for their defence.
Japan relies on the US military to defend itself, but its presence is a delicate subject in the country.
The Japanese public have voiced anger over crimes and accidents, particularly concerning sexual violence in the southern island of Okinawa, where most of the US troops are based.
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