The head of the contingent, Brigadier-General Jovito Palparan, arrived early on Monday morning on a commercial flight in advance of the remaining 50 troops who are due to return this week.
The withdrawal meets a deadline of 20 July set by the captors of Filipino truck driver Angelo de la Cruz. They threatened to kill him unless Manila withdrew from Iraq.
"I am happy to be back," Palparan told reporters at Manila's international airport.
An air force official said ten troops who left Iraq last Friday had not boarded their scheduled flight from Kuwait on Monday, but would be home within days.
The remaining 40 troops were due to leave for Kuwait on Monday as announced by the Foreign Ministry on Sunday.
De la Cruz's family has prepared
a warm welcome home
"We just hope that the Iraqi militants will keep their promise of releasing Angelo since the humanitarian contingent have already pulled out," Beth, one of his sisters, told reporters on Monday.
De la Cruz's family and friends have prepared a warm welcome, tying yellow ribbons around the village. A local construction firm is building the impoverished family a new house.
There was still no word on the release of de la Cruz, who was last seen in a video shown by Aljazeera satellite channel on Thursday in which he said he would be coming home.
Nearly two weeks after de la Cruz was abducted while driving fuel into Iraq from Saudi Arabia, relatives in his village of Buenavista, north of Manila, were optimistic he would be home soon.
President Gloria Macapagal Arroyo's decision to withdraw a month earlier than planned has drawn heavy criticism from the United States and several other allies, who have said it sets a bad precedent for giving in to the demands of the captors.
"Had the president allowed de la Cruz
to be beheaded,
she would have sent
the wrong signal"
Neal Cruz, columnist,
Philippine Daily Inquirer
But her popular ratings seem unlikely to be dented at home by the end of a deployment that was not particularly popular despite the Philippines' long-standing ties with the United States.
Left-wing groups had staged small but noisy protests calling for the troops' withdrawal and Arroyo faced broad pressure to secure de la Cruz's release as he became a symbol of the eight million Filipinos working abroad to support poor families at home.
"Had the president allowed de la Cruz to be beheaded, she would have sent the wrong signal," columnist Neal Cruz wrote in the Philippine Daily Inquirer.
"The message: that the government really doesn't care for the OFWs (Overseas Filipino workers). That calling them heroes is only lip service."