Japanese foreign minister Fumio Kishida said his country was considering making stronger protests "at a higher level" after China announced Saturday it was setting up the zone over an area that includes Tokyo-controlled islands claimed by Beijing.
US secretary of state John Kerry and secretary of defence Chuck Hagel said on Saturday they were "deeply concerned" at China's move and were committed to defending Japan.
China said it was setting up the "air defence identification zone" over an area including the islands in the East China Sea to guard against "potential air threats".
It released a set of aircraft identification rules that must be followed by planes entering the area.
Kishida told reporters Japan cannot accept the Chinese measure, calling it "a one-sided action which leads us to assume the danger of unpredictable events on the spot".
In Seoul, South Korea's defence ministry said the Chinese zone partly overlapped its own.
"We find it regretful that China's air defence zone partly overlaps with our military's Korean Air Defense Identification Zone (KADIZ) in the area west of Jeju Island," said a ministry statement, according to Yonhap news agency.
"We will discuss with China the issue so as to prevent its establishment from affecting our national interests."
A military source quoted by Yonhap said the overlapping area is 20 km wide and 115 km long.
The Chinese zone also includes the South Korean-controlled submerged rock that lies within the two countries' overlapping economic zones, according to a defence ministry official quoted by the news agency.
The dispute over the islands, known as the Senkakus in Japan and the Diaoyus in China, heated up last year when Japan's government bought some of them from a private owner.
China has since sent coastguard vessels and other state-owned ships as well as aircraft close to the islands, sometimes breaching airspace and territorial waters around them.
This has prompted Japanese coastguard boats and air force fighter jets to try to warn them off.
The Japanese defence ministry said Saturday two Chinese planes entered Japan's own air defence identification zone over the East China Sea, prompting its air defence force to scramble fighter aircraft.
The ministry lodged a strong protest with a minister at the Chinese embassy in Tokyo by telephone.
Defense secretary Hagel reiterated that the islands fall under the US-Japan security treaty, meaning that Washington would defend its ally Tokyo if the area is attacked.
He made it clear that the United States, which stations more than 70,000 troops in Japan and South Korea, would not respect China's declaration of control over the zone.
However Washington has repeatedly said it takes no position on the islands' ultimate sovereignty.
Japan has vowed not to cede sovereignty or even to acknowledge a dispute with China over the islands.
It accuses its neighbour of trying to change the status quo through intimidation.
Former Japanese foreign minister Masahiko Komura, speaking as deputy head of the ruling Liberal Democratic Party, said defence officials of the two countries must keep in close communication "to prevent a touch-and-go situation from arising".
"China used to maintain a certain degree of restraint in the past although it insisted that the Senkaku islands were part of its territory," Komura, who served as foreign minister from 1998-1999 and from 2007-2008, told public broadcaster NHK.
"But it is a serious matter that Chinese ships have recently intruded into the territorial waters and that China declared the air defence identification zone this time."