Hagel had criticised China's Air Defence Identification Zone (ADIZ) in the East China Sea as "provocative and unilateral" in an interview with the Japanese media ahead of his arrival here.
He had also brought up the "growing US concern" about territorial disputes in the South China Sea during talks with defence ministers of the Association of Southeast Asian Nations (ASEAN) in Hawaii last week.
"I can tell you frankly, your remarks made in the ASEAN defence ministers meeting and to Japanese politicians were tough, and with a clear attitude," Fan Changlong, vice-chairman of China's Central Military Commission, told Hagel during their joint press briefing here last night.
In November, China unilaterally declared an ADIZ over a swath of the East China Sea, including a disputed island chain known as Daioyu in China and Senkaku in Japan.
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The Pentagon chief has publicly backed Japan's claim on the Daioyu and welcomed Tokyo's review of the self-defence aspect of its constitution.
On the South China Sea issue, China holds a consistent claim.
"But Secretary Hagel is partial to the Philippines and pointed fingers at China, though the Philippines occupied some of China's reefs," Fan was quoted as saying by the state-run Xinhua news agency.
"China hopes the US can be a responsible great power and do more to promote regional stability and the friendship between the two countries and militaries," Fan said.
He called on the Chinese and US militaries to cherish development and move towards a stable and healthy military relations.
Hagel thanked Fan for being straightforward and candid.
The US has had a One-China policy since 1979 and supports the peaceful reunification of Taiwan and the Chinese mainland. A bill by a particular committee of Congress does not represent government policy, Hagel said.
Hagel is on a 10-day visit to Japan, China and Mongolia.