The Philippine coastguard said on Sunday that it had been ordered to prepare two ferries, the Batangas and Pampanga, for the 15-day voyage to Lebanon.
The coastguard ferries, each capable of carrying 300 people, will leave Manila on Wednesday for the 6,568 nautical mile voyage.
A coastguard spokesman, lieutenant commander Joseph Coyme, said the president, Gloria Arroyo, had approved the mission in a bid to evacuate thousands of Filipinos stranded in Lebanon.
He said Filipinos will also be taken to Cyprus or ports in Turkey, Egypt or Syria for repatriation.
On Friday, Arroyo made an appeal for the estimated 30,000 Filipinos working in Lebanon to leave, saying the conflict was set to escalate.
Filipinos typically work in menial jobs in Lebanon and most are women working as maids with limited incomes.
Esteban Conejos, the country's foreign affairs undersecretary, said in a statement on Sunday that Manila was securing the "proper clearance" from Israel to allow the vessels to approach Lebanese ports.
The Israeli navy has maintained a total blockade on all Lebanese ports since Israel began its offensive against Hezbollah positions in the south of the country last month.
Conejos said about 450 Filipinos were able to flee Beirut on Saturday to northern Syria using a coastal land route aboard buses.
So far, 2,652 overseas Filipino workers have arrived back in the Philippines from Lebanon using the land route to Syria.
The coastguard spokesman said the sea route had become the only practical and safe option left for the government.
"The land route to Syria is no longer safe," he said.
Most foreigners living in Lebanon have already been evacuated since Israel launched a fierce offensive against the Lebanese Shia militia Hezbollah which captured two Israeli soldiers in a cross-border raid on July 12.