MANILA, June 1 (Reuters) - President Gloria Macapagal Arroyo said on Friday the Philippines' new security pact with Australia would make the Southeast Asian region safer and more secure from Islamic militants.

Arroyo said the defence arrangement with Canberra allowing elite Australian commandos to train local troops would "help us fight terrorists lurking in swamps and shadows of remote southern islands".

"By working together on a regional basis, we hope to make our country and the entire region safer and more secure for our God-fearing people," Arroyo said in a statement on her arrival from a five-day visit to New Zealand and Australia.

"Let us not send mixed messages to the world. Rather, let us say with one voice that says the Philippines is on the move. It is a worthy partner in peace and a prime location for investment."

On Thursday, the Philippine and Australian defence ministers signed a defence deal that will clear the way for Australian troops to train Filipino counterparts on the troubled southern island of Mindanao.

Philippine security officials said Islamic militants from neighbouring Indonesia and Malaysia had been seeking refuge on Mindanao, protected by Muslim rebels fighting to set up a separate and independent Islamic state in the south.

Western and Philippine intelligence officials believe there are about 30 to 40 Indonesian, Malaysian and Singaporean Muslim militants belonging to Jemaah Islamiah and other jihadist groups hiding in the south.

Umar Patek and Dulmatin, two top Islamic militants who were blamed for the 2002 bombings on the Indonesian resort island of Bali that killed 202 people, mostly Australian tourists, had been on the run in the south.

Since August 2006, about 8,000 soldiers, backed by U.S. military intelligence and logistics, have been tracking down 400 Abu Sayyaf militants sheltering Dulmatin and Umar Patek on the tiny island of Jolo.

Australia has promised to provide $4 million worth of river boats to patrol shallow marshlands in the south where suspected Muslim militants are hiding.

An extra $3.2 million was also allocated every year to fund advanced training and military education of Filipino soldiers in Australian war colleges and army schools.

Australia has been trying to build security ties with Southeast Asian nations to crack down on Jemaah Islamiah.

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