"Americans are very appreciative to the people... and the president of the Philippines for the support that your country is providing in the global war against terrorism," he said.
As undersecretary, Brownlee is responsible for training, supplying, equipping and overseeing the budget of the US army.
Cmdr. John Fleming, a spokesman for US troops, said Brownlee will talk with US Special Forces members training Filipino troops who are hunting the Abu Sayyaf terrorist group which has been linked with Osama bin Ladens terrorist network.
"Its his first opportunity to see how were involved and how were engaged in the training and assisting and advising of our counterparts," he said.
The Abu Sayyaf have been holding American missionary couple Martin and Gracia Burnham and Filipino nurse Deborah Yap for almost a year now.
Brownlee flew to Basilan to personally assess the military exercise in which US Special Forces have been training and advising Filipino troops on counter-terrorism.
Brownlees trip is part of an Asia-Pacific familiarization tour.
Before flying to Zamboanga City, he had been to South Korea for two days.
Capt. Julio Servando, Armed Forces Southern Command spokesman, said the military exercise has stopped terrorists fleeing US forces in Afghanistan from entering the country.
"This explains there are arrests being made in the areas right now and we are able to monitor the activities of the terrorist network and cell not only operating in Central Mindanao and other parts of the country," he said.
Servando said they have not monitored the movement of any al-Qaeda terrorist but that the military is now uncovering their activities.
"Somehow this contributes to the neutralization of the elements with the conduct of the exercise," he said. "Because we were able now to share such intelligence information to our US counterparts through the intelligence fusion which is part of the exercise."