Admiral Samuel Locklear, who oversees American forces across Asia as head of Pacific Command, gave the estimate a day after the United States pushed for a resolution committing major powers to block the movement of foreign fighters to Iraq and Syria.
"It certainly is an issue that were paying very close attention to today," Locklear told a press conference in Washington.
"Theres probably been about 1,000 potential aspiring fighters that have moved from this region, based on kind of our overall assessment.
"That number could get larger as we go forward, but certainly thats about the size or the magnitude that we perceive at this point in time," the admiral said.
Locklear also said the expanded air war against the IS group in Iraq and Syria did not mean a strategic US "rebalance" to the Asia-Pacific would be scaled back, saying that the American military would continue to pursue its plan to bolster its presence and defense ties in the area.
President Barack Obama underscored growing concerns about foreign fighters flocking to the Middle East at a special session of the UN Security Council on Thursday.
Obama chaired the meeting that saw the adoption of a resolution demanding governments prevent recruitment and all forms of aid to foreign fighters, making it illegal to collect funds or help organize their travel.
An Islamist militant band in the Philippines, Abu Sayyaf, has threatened to kill one of two German hostages unless a ransom is paid and Berlin withdraws its support of a US-led air war against the IS group in Iraq and Syria.
The Abu Sayyaf, considered a "foreign terrorist organization" by the United States, is a loose band of several hundred Islamic militants originally organized with Al-Qaeda funding in the 1990s.
Manila has said Abu Sayyaf has no genuine connection to the IS jihadists and is merely trying to cash in by proclaiming allegiance to the group.
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