Iwaya also told Wang Yi in Beijing that "Japan is closely monitoring the Taiwan situation and recent military developments", a Japanese foreign ministry statement said.
China regards Taiwan as its territory and has not ruled out using force to bring it under its control.
Taipei said earlier this month that Beijing had held its biggest maritime drills in years, stretching from near the southern islands of Japan to the South China Sea.
Iwaya "expressed serious concerns over the East China Sea situation, including around the Senkaku Islands (and) China's increasing military activity," the statement said.
The chain of uninhabited islands claimed by Beijing but administered by Tokyo are known as the Diaoyu in China.
The Japanese minister also raised concern over "China's unilateral resources development".
The bilateral talks and Iwaya's working lunch with Wang lasted three hours, the statement said.
The ministers agreed to realise "foreign minister Wang's visit to Japan at the earliest and most appropriate timing next year" to hold "high-level economic dialogue".
China and Japan are key trading partners, but friction over disputed territories and military spending has frayed ties in recent years.
China also in August formally indicted a Japanese man held since last year on espionage charges.
Iwaya "pointed out that the detention of Japanese citizen(s) and the opacity surrounding the anti-espionage law are causing Japanese people to think twice about visiting China, and called for the improved transparency and swift release of detained Japanese national(s)", the statement said.
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