Ms Bishop and Australia's Defence Minister, David Johnston, have held talks in Toyko with their Japanese counterparts to deepen defence and security cooperation.
It comes at a sensitive time, with heightened tensions between Japan and China over a territorial dispute in the East China Sea.
Speaking to Sky News, Ms Bishop said Australia does not take a position on the merits of sovereignty claims in the area and Australia still has good relations with China.
"Support for Japan in this area does not apply a weakening of our commitment to our relationship with China or any other country," she said.
"It's not a zero sum game. We maintain positive and mutually supporting bilateral relationships with both China and Japan."
The ministers were meeting their opposite numbers in Tokyo for the fifth Australia-Japan Foreign and Defence Ministerial (2+2) Consultations.
The meeting follows Prime Minister Tony Abbott's visit to Japan in April, where he agreed on both a trade deal and future cooperation on defence science and technology, particularly joint research on marine hydrodynamics.
In practice, that means submarines. Australia is interested in Japan's new Soryu-class boats as it looks to replacements for the Navy's six Collins submarines.
The ministers are expected to conclude negotiations on the proposed Defence Science, Technology and Materiel Agreement announced during Mr Abbott's visit.
The agreement will allow Australia and Japan to jointly develop defence technologies, establishing a basis to deepen defence cooperation, they said.
During the visit, Ms Bishop has met with Foreign Minister Fumio Kishida and other senior Japanese ministers, parliament members and academics to discuss international and bilateral developments.
Among the issues discussed was the New Colombo Plan, under which students from around the region will receive scholarships to study in Australia.
Senator Johnston has met with Japanese Defence Minister Itsunori Onodera separately to discuss progress in bilateral defence engagement.
"We discussed a number of proposals for further deepening defence, security relationship," he said. "These proposals cover the full range of defence activities, including bilateral exercises, technology co-operation; and we will put them forward to our prime ministers for their consideration."
He said both countries share a common interest in a secure, stable and peaceful region.
Japanese Prime Minister Shinzo Abe, who reportedly is planning to visit Australia in July, wants Japan to play a bigger role on the global stage, loosening longstanding constitutional restrictions on the role of its defence force.
He has moved to ease tight restrictions on weapons exports, paving the way for greater defence co-operation with Australia.
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