Philippine Foreign Undersecretary Jose Brillantes said in a written statement on Friday that the three-member mission, led by charge d'affaires Eric Endaya, had arrived at the embassy in Amman where they would be posted "for an indefinite period of time,"
"The diplomats in Baghdad are in Amman for security reasons occasioned by the recent kidnappings of diplomats," he added.
The al-Qaida group in Iraq has said it murdered two Algerian diplomats it kidnapped last week.
The reported killings followed the abduction and murder of Egypt's top envoy in Baghdad in early July.
More than 6000 Filipinos work in Iraq, many of them civilians in US military outposts, despite a ban on working there imposed last year by Manila after a Filipino truck driver was kidnapped by Iraqi armed groups.
The truck driver was released unharmed after the Philippines withdrew its small military contingent taking part in the US-led coalition.
Brillantes said a Philippine travel ban to Iraq "remains in force."