Ships and a total of nearly 900 troops from the United States, France, Australia and host Japan and observers from 15 other countries took part in the "Team Samurai" drill, the first of its kind in Asia.
"We are sending a signal to everybody who wants to traffic weapons of mass destruction that we have zero tolerance for that," said John Bolton, US undersecretary of state for arms control and international security.
He said that while the United States had concerns with alleged proliferation by China, which did not take part in the drill, the chief suspect was North Korea.
"North Korea is a serious proliferation problem and it's the world's foremost proliferator of ballistic missile technology," Bolton told reporters.
He said the exercise showed the determination of the "civilized world" not to allow "the world's most dangerous weapons to fall into the hands of the world's most dangerous people".
On a rainy morning a US vessel handed over a cache of "chemical weapons" to a Japanese boat in Sagami Bay, 50 kilometers (30 miles) south of Tokyo, triggering a high-speed chase by Australian, French, Japanese and US ships.
As five helicopters roared overhead, the Japanese coast guard shot a red powder at the suspected ship to signal it to stop.
Multinational inspectors, some in chemical-proof suits, searched and seized suspicious material from the cabin, which was sealed off with yellow tape by the Australian coast guard.
The drill, known as the Proliferation Security Initiative (PSI), was launched by US President George W. Bush in May 2003 to improve global coordination to intercept weapons shipments by rogue states and terrorist groups.
The United States has said the drills elsewhere helped persuade Libya to give up its program to develop weapons of mass destruction and provided intelligence that broke up the network of Abdul Qadeer Khan, the father of Pakistan's atomic bomb accused of assisting North Korea, Iran and Libya.
Stalinist North Korea, which has exported missiles and claims to be developing nuclear weapons, said the exercise showed a "US strategy to militarily blockade and stifle" it.
"This is a serious infringement upon the sovereignty of the DPRK (North Korea) and an intolerable military provocation to it," the official Korean Central News Agency said Monday.
Amid the blistering criticism, North Korea's neighbors China and South Korea did not respond to invitations to take part in the exercise.
North Korea is refusing to re-enter six-nation talks on its nuclear program.
The North Korean statement Monday said: "These moves only make the prospect of the negotiations ... dimmer as the days go by. Dialogue can never go together with war exercises."
Australian Army Colonel Mark Hoare said in Sagami Bay that "this is not an exercise targetting any country.
"Proliferation of weapons of mass destruction is a big concern for the international community and Australia," Hoare said.
French Air Force Colonel Maurice Dumond said France's "concern against proliferation is very strong and we fully support all these initiatives".
It is the 12th time the weapons drill has been held but the first time in Asia.
In the Japanese version, the seized material is Sarin -- the nerve gas spread in the Tokyo subway in 1995 by the Aum Supreme Truth cult which killed 12 people and injured more than 5,000.