Wu Hsin-Hsing will "work in close cooperation with the Philippine government and people to further strengthen the existing ties between the peoples and countries," a statement from the mission said.
Manila does not have formal diplomatic ties with Taiwan because of its so-called "One China" policy. Beijing considers Taiwan a rebel province.
Wu replaced Benjamin J.Y. Lo, who was reassigned to the ministry of foreign affairs after completing his tour of duty.
He said he has been encouraging Taiwanese businessmen to invest in the Philippines.
Taiwan is the Philippines’ fourth largest trading partner next to the United States, Japan and Singapore. Trade between the two countries reached $5.6 billion in favor of the Philippines.
"We know that both sides have a very strong hope in community development," Wu told reporters upon his arrival at Ninoy Aquino International Airport.
"I have already talked with our country’s major entrepreneur and business companies, and their response is very positive and very good," he said.
"We all know that Taiwan and the Philippines both show strength and cooperation in agriculture. I know that the Philippines is very, very good in agricultural projects and Taiwan is very interested about these."
Wu also wants to strengthen cultural and religious ties, noting that Taiwan hosts 18,000 Filipino overseas workers, most of whom are Catholics.
Taiwan, which is mainly Buddhist, has a sizable Catholic community.
Wu also wants to boost tourism in both countries. At least 80,000 Taiwanese visit the Philippines annually, he said.
"Right now it is time that we would like to invite many Filipinos who can go to Taiwan and to see also our beautiful island," he said.
"I also would like to take this opportunity to say hello to all Filipinos and also to all the Chinese and Taiwanese people who live in this country, and I look forward to seeing you in the future."
Wu came with his wife Chow Ding Yi, eight-year-old son Wu Shang-His and five-year-old daughter Wu Shang Ann.
They were met by Antonio Basilio, chairman of the Manila Economic and Cultural Office, representatives of the local Taiwanese community, Filipino-Chinese businessmen, among others.
Wu will pay President Arroyo a courtesy call maybe this weekend.
Wu’s assignment to the Philippines "is an indication of much importance Taiwan places on their bilateral relations with the Philippines. So our relationship has been going and strengthening over the years," Basilio said.
Wu was the vice minister of the Overseas Chinese Affairs Commission prior to his current assignment, according to the TECO.
He served as deputy secretary-general of the Straits Exchange Foundation, Taiwan’s semi-official organization in charge of negotiations and exchanges with China, from 1998 to 2000.
Wu has authored four books on Chinese-Taiwanese relations, as well as over 200 academic and newspaper articles and book reviews.