"The Department of Foreign Affairs has issued Alert Level 3 (voluntary repatriation phase) for Afghanistan due to the heightened tensions in that country following the conduct of the presidential elections last June 14," it said in a statement.
"With this announcement, Filipinos in Afghanistan are strongly encouraged to volunteer to return to the Philippines."
The election stand-off has sparked concern that protests could spiral into ethnic violence and even lead to a return to the fighting between warlords that ravaged Afghanistan during the 1992-1996 civil war.
On Tuesday, presidential candidate Abdullah Abdullah claimed victory, blaming fraud for putting him behind rival Ashraf Ghani in preliminary results.
The Philippines has an existing travel ban to the war-torn nation, but the government acknowledges this has failed to stop Filipino civilians going there, often by way of third countries, for relatively high-paying jobs inside US military bases.
An estimated 4,000 Filipinos are now working for US contractors in Afghanistan, foreign department spokesman Charles Jose told AFP.
The Philippines does not maintain an embassy in Kabul, with its diplomatic representation in that country under the Filipino mission in Pakistan, he added.
About 10 million Filipinos live or work abroad, a tenth of the population, to escape widespread poverty and scant job opportunities at home.