Foreign Secretary Albert del Rosario was heading to neighbouring Tunisia to organise an evacuation as fighting resumed between militias seeking to control the Libyan capital's crippled international airport.
Mr Del Rosario said he was repeating a 2011 mission that evacuated thousands of Filipino workers during the uprising that toppled Libyan dictator Moamer Kadhafi.
"Our major challenge, as in 2011, is to convince our folks that they must leave Libya at the soonest time to avoid the perils of a highly exacerbating situation there," he told reporters in Manila.
The Philippines ordered an evacuation on July 20, hours after the discovery in the eastern city of Benghazi of the beheaded remains of a Filipino construction worker who had been abducted.
It also imposed a travel ban to the North African country, which has been plagued by violence since Kadhafi's overthrow.
On Wednesday, a Filipina nurse was abducted by a gang of youths outside her residence in Tripoli and gang-raped, the foreign department said.
She was released about two hours later and a Filipino consular team took her to hospital for treatment.
"We condemn these crimes that have been committed against our people," President Benigno Aquino's spokesman Herminio Coloma told reporters in Manila.
Despite the dangers, Mr del Rosario said many of the Filipinos, mostly employed in construction and hospitals, are refusing to leave because they would be unemployed back home.
Only a few more than 700 had left Libya by Wednesday, according to the foreign ministry, despite the rapidly deteriorating situation as warring militias battle for control of key population centres.
Mr Del Rosario said he is flying to Tunisia's Djerba island to "try to convince our people to leave (Libya) because the situation there is very dangerous.
"We are in the process of engaging ships from Malta that would pick up our people from Benghazi, Misrata and hopefully Tripoli then return to Malta for air transport to Manila," he said.
While each vessel could carry up to 1,500 people, he said the government was still negotiating safe passage through these ports.
Failing that, the Filipinos would be bused to Tunisia, where flight arrangements would be made, he added.
Fighting resumes at airport
Mr Del Rosario could not have flown in to Tripoli if he had wanted to, because the airport was knocked out of commission by fighting earlier this month.
Another round of clashes erupted on Thursday, airport security chief Al-Jilani al-Dahech told AFP, with attackers assaulting the facility using both small arms and heavy weapons.
Mr Dahech said some of his men had been wounded, but gave no details.
At least 100 people have reportedly been killed and 400 wounded since July 13 when the airport battle erupted.
Witnesses said there was also fighting on the road to the airport and in a western suburb of the capital on Thursday, while numerous explosions were heard in the city centre.
The Tripoli clashes, the most violent since Kadhafi's ouster, started with an assault on the airport by a coalition of groups, mainly Islamists, which has since been backed by fighters from third city Misrata.
The attackers are battling to flush out fellow former rebels from the hill town of Zintan, southwest of Tripoli, who have controlled the airport for the past three years.
The violence, also raging in Benghazi, prompted Britain, France, Germany and the Netherlands to join Washington in urging their citizens to leave as soon as possible.
The United States pulled its diplomatic staff out under air cover on Saturday.
Belgium, Malta, Spain and Turkey previously urged their nationals to leave.
Meanwhile, firefighters were still battling a blaze at a fuel depot near the airport that broke out Sunday after a rocket hit a storage tank.
More than 90 million litres of fuel are stored in the facility, which also houses a natural gas reservoir.