Amid an economic slowdown, Koizumi has vowed to carry out drastic fiscal reforms by cutting spending, including official development aid (ODA).
It raised the prospect that the worlds biggest aid budget totaling more than $8.46 billion for the fiscal year to March 2002, would be cut.
"We hope that we will not be included in the cut," Mrs. Arroyo said in a statement yesterday.
Tokyo is Manilas major ODA source, contributing $6.3 billion or 45 percent of the total received by the Philippines between 1992 and 1999.
Tokyo reported last week that the worlds second biggest economy shrank 0.8 percent in the three months to June from the previous quarter.
Filipino analysts say Manila is also concerned the economic slump could lead to Japanese firms scaling back their overseas investments, including those in the Philippines.
"We would like to show the Japanese people that under this administration, we have been using the ODA very efficiently," Mrs. Arroyo said.
"The utilization is much more efficient, because we realize that the Japanese taxpayers are working hard for this ODA, and we dont want it to go to waste," she said.
Japanese Foreign Minister Makiko Tanaka said in July that Japan must have the courage to withdraw from its overseas projects if they prove to be "useless."
Mrs. Arroyo is to make a four-day "working visit" to Japan beginning Wednesday, the presidential palace said.
She is scheduled to call on Emperor Akihito and Empress Michiko at the Imperial Palace, speak at three business meetings and hold bilateral talks with Koizumi.
Mrs. Arroyo believes Japan "should really play a bigger role in the region and in the world," the palace statement said.
"We want to expand our relationship not only in economic or ODA relationship but also in political and security relationship," she added.