Foreign Secretary Delia Albert on Friday said the remaining members of the 51-strong contingent would be pulled out of Iraq shortly.
"The Philippines government has recalled the head of its humanitarian contingent from Iraq. He is leaving Iraq today with other 10 members of the contingent," Albert said.
"The rest of the members will be out of Iraq shortly," he said.
The secretary said the government was continuing its efforts to secure the release of captured truck driver Angelo de la Cruz.
The group holding Angelo has threatened to behead him unless the Philippines withdraws its forces from Iraq.
The group first laid down 20 July as the deadline by which the Philippines had to pull out its force. But in a message aired on Aljazeera on Thursday, the deadline was extended until 1 August.
Aljazeera also broadcast a video of Angelo, begging his government to bring forward the planned departure date of its forces.