The quota will cover an initial period of two years, Tetsuo Tsuji, the administrative vice labor minister, told a news conference.
"We consider the numbers appropriate in the sense that they will not have an adverse effect on the labor market in Japan," he said.
While small in number, it marked the first time that Japan, which strictly controls immigration, has accepted foreign workers as part of a bilateral trade pact.
Japan has also been holding talks with Indonesia and other Asian countries on admitting nurses and caregivers.
The deal was signed in Helsinki on Saturday by Japanese Prime Minister Junichiro Koizumi and President Arroyo ahead of a meeting there of Asian and European leaders.
Under the agreement, the 1,000 Filipina nurses and caregivers will be allowed to work in Japan on condition they pass Japanese qualification examinations.
Candidates for the jobs will be selected by the Philippine government and study the Japanese language for six months in Japan before they receive on-the-job training, Tsuji said.
If they obtain Japanese state licenses for the jobs within time limits — three years for nurses and four years for caregivers — they will be allowed to work in Japan on a long-term basis.
Japan, Asia’s largest economy, is expected to face a growing need for caregivers as its population is rapidly graying.
Eight million Filipinos — 10 percent of the population — work overseas and sent home $10.7 billion last year.
The Philippines protested last year after Japan tightened visa regulations to crack down on sex workers amid fears that the restrictions would also affect legitimate workers.