Vice Minister of Defence Kenji Wakamiya was in Ishigaki on Thursday to explain to Mayor Yoshitaka Nakayama a plan to deploy about 500 ground troops near the disputed East China Sea islands.
The plan beginning in 2019 aims to station troops intended for emergency response in case nearby islands are infiltrated or for missile defense.
Japan has escalated its defence readiness as China has increased its military buildup and patrols near the islands.
Ishigaki has jurisdiction over the Japanese-controlled Senkaku islands that China also claims and calls the Diaoyu islands.
Japan, whose concerns over security have depeened amid China and North Korea's missile and nuclear weapons ambitions, is already building a base on the nearby island of Yonaguni to deploy 150 coastal monitoring troops, and aims to deploy hundreds more on both the Miyako and Amamioshima islands by 2018.
According to Japanese coastguard statistics Chinese government vessels intrude into Japanese-claimed territorial waters surrounding the disputed islands several times a month.
The country has approached those waters nearly every day since Japan nationalised some of the disputed islands in September 2012.
Japanese Prime Minister Shinzo Abe's hawkish government passed new security laws in September, although the opponents said they violate Japan's pacifist constitution.
According to Japanese media reports Japan and China are due hold maritime security meetings in Xiamen in December to discuss some of the oustanding issues between the countries and ways to avoid security conflicts.
The disputed waters, partially or totally claimed by Vietnam, Malaysia, the Philippines, Taiwan and Brunei, have also become the stage for a competition over regional superiority between the world's two largest economic and military powers, Beijing and Washington.