Navy planners on the new humanitarian mission were considering possibly coordinating their operations with the Medical Civil Action Program (MEDCAP) being run by American special operations units in the southern Philippines.
"I think we are still looking into the possibility of doing that," mission commander Capt. James Morgan told reporters on Tuesday.
Members of the Joint Special Operations Task Force-Southern Philippines have been supporting Philippine-led counterterrorism operations against al Qaeda-linked terror group Abu Sayyaf since 2002.
The task force is one of the longest-running U.S. counterterror missions in the Pacific.
The Navy's hospital ship Mercy will spend four months in the Pacific as part of the latest iteration of the Pacific Partnership mission.
The ship will make port calls in Indonesia, the Philippines, Vietnam and Cambodia as part of Pacific Partnership 2012.
Navy medical specialists plan to carry out humanitarian support operations alongside their military and civilian counterparts in each country, Morgan said.
Mission leaders also will liaison with their counterparts in each country, to exchange lessons learned from previous U.S-led humanitarian operations in Haiti and Japan.
While mission planners may link up with members of the special operations task force in the Philippines, it will not play a role in a large-scale war game now under way between Washington and Manila in southern Philippines.
Morgan said the Philippine leg of the Pacific Partnership mission would be "wholly separate" from the U.S.-Filipino wargame.
"This is a mission that has been [planned] for a long time," he said.
The four-month humanitarian operation is the latest in a string of recent efforts taken on by the department to shift American military focus from the Middle East to the Pacific.
That shift was a key part in the White House's new national security strategy rolled out in February by President Obama.
In April, the first tranche of a 200-man Marine Corps force arrived at the service's new base in Darwin, Australia.
Deputy Marine Corps Commandant Gen. Joseph Dunford said during a March 29 speech that along with the Darwin base, the service was planning to increase its presence in the Philippines.
Those additional deployments would be temporary and would not require any permanent Marine Corps installations in the country, Dunford said at the time.
But local news reports out of Manila claim the Philippines is already building a new facility to house the incoming Marines.
A new seaport being built by the Philippine government in the Spratly Islands could become the Pentagon's military outpost in the hotly contested South China Sea, according to those reports.
The South China Sea has become a point of contention between China and its regional neighbors, with the Asian superpower using its increasing military muscle to exert control over the area.
On April 12, Beijing sent three warships to a section of the South China Sea, off the northwest coast of the Philippines, to support a Chinese fishing ship being detained by the Philippine navy.
Claiming territorial sovereignty over the costal waters where the Chinese fishing vessel was detained, Manila has deployed an additional warship to the area.