Shinzo Abe's warning comes after Washington said it would stand by him in the event of any military clash over the Senkaku Islands, which Beijing claims as the Diaoyus. JPN/Agencies
"I am strongly concerned as it is a profoundly dangerous act that may cause unintended consequences," Abe told the Parliament, reports said.
"Japan will ask China to restrain itself while we continue cooperating with the international community," Abe said.
The comments are the first from the premier on the issue since Beijing on Saturday announced it would require all aircraft flying over an area of the East China Sea to obey its orders.
US Secretary of State John Kerry declared Washington "deeply concerned", saying the move raised "risks of an incident".
"This unilateral action constitutes an attempt to change the status quo in the East China Sea," Kerry said.
The announcement of the area, which also includes waters claimed by Taipei and Seoul, provoked ire in both cities, with South Korean Defence Ministry spokesman Kim Min-Seok saying it was "regrettable".
Part of the zone overlaps South Korea's own air defence zone and incorporates a disputed, submerged, South Korean-controlled rock -- known as Ieodo -- that has long been a source of diplomatic tension with Beijing.
"I'd like to say once again that we have unchanging territorial control over Ieodo," Kim said.
Japan's Foreign Ministry said it would not respect the Chinese demarcation, which it said had "no validity whatsoever in Japan".
China dismisses US, Japan objections
Meanwhile, China has termed the objections raised by Japan and the US on its move as "absolutely groundless and unacceptable", and lodged a protest with Washington objecting to its criticism.
Reacting to the protests lodged by Japan over the creation of the East China Sea Air Defence Identification Zone, Chinese Defence Ministry spokesman Yang Yujun said Japan's remarks are "utterly groundless and China won't accept them."
He also termed US criticism of the zone as groundless, state-run news agency quoted him as saying. The United States is now raising opposition and blaming China which is totally groundless, Yang said.
The Foreign Affairs Office of China's Defence Ministry has lodged solemn representations with the military attache of the US Embassy in China yesterday, Yang said.
"The establishment of the East China Sea Air Defence Identification Zone by the Chinese government is "totally rational and indisputable," he stressed.
According to Yang, 20-plus countries, including the United States, have set up their own air defence identification zones since the 1950s.
Beijing is engaged in a series of bilateral tiffs over the ownership of islands and the waters surrounding them, including several separate disputes in the South China Sea. But the most serious, and the one that analysts say has the potential to turn into an armed confrontation, is with Japan over the archipelago in the East China Sea.
The disagreement has simmered for decades, but snapped sharply into focus in September 2012 when Tokyo nationalized three of the islands.
Japan billed the move as an attempt to avoid a much more inflammatory purchase by a vocal nationalist, but China reacted with fury and relations went into meltdown. The two countries now play an almost permanent game of cat and mouse in the area, with official ships and aircraft shadowing each other and warning the other side to leave.
Observers say the frequent presence of military or paramilitary bodies from both sides raises the risk that a miscalculation or a crash could quickly escalate into a conflict, dragging in the United States.
Shinzo Abe's warning comes after Washington said it would stand by him in the event of any military clash over the Senkaku Islands, which Beijing claims as the Diaoyus.