The troops will beef up Japan's first military deployment since World War II in a country where fighting is still under way.
Police carried submachine guns at airports in and around Tokyo and Osaka as part of tightened security measures at 650 important facilities around the country, including Prime Minister Junichiro Koizumi's official residence and the US embassy in Tokyo.
The National Police Agency said that, in response to fears of a terror attack against the dispatch of Japanese troops to Iraq, security would be brought to the highest level since the US-led war on Iraq in March last year.
Two Japanese diplomats were killed last November in an ambush in northern Iraq, after repeated threats of attacks against Japanese troops from an alleged spokesman for the al-Qaida group.
After training in Kuwait, the latest army contingent will move to Samawa, southern Iraq, to join earlier Japanese deployments there on a mission to perform non-military "humanitarian and reconstruction" work.
Japanese troops will be engaged
in mainly non-military work
The group left the airport in Chitose on the northern island of Hokkaido by a special government plane.
Around 100 Japanese ground troops are already in Samawa, 270km south of Baghdad.
A total of 600 Japanese ground troops will be in Iraq by the end of March, with logistical support from around 400 air force and naval personnel in the region.
According to opinion polls, about half of the Japanese are opposed to the troop dispatch which they believe runs contrary to the country's post-World War II constitution which bans the use of force in settling international disputes.
Annan in Tokyo
UN Secretary General Kofi Annan arrived in Tokyo on Saturday on a five-day visit for talks with Japanese leaders on ways to reform the world body and help war-torn Iraq with its reconstruction.
Annan will address the Japanese
parliament on Tuesday
He is scheduled to hold talks with Koizumi and Foreign Minister Yoriko Kawaguchi during the visit, officials said.
On Tuesday, he will deliver an address to the Japanese parliament, the first by a UN chief.
Annan said before his departure from New York on Friday that a host of issues would be on the agenda during his trip that comes amid grumbling from Tokyo that it is paying too much towards the United Nations budget and getting too little in return.
Tokyo is also hoping to win a permanent seat on the UN Security Council if and when a long-discussed move to reform and expand the prestigious body gets carried through.
Japan's foreign ministry announced last month it wanted to slash its payments when assessments are reviewed three years from now.