Foreign Secretary Albert del Rosario said it would pick up Filipinos from Misrata and Benghazi and hopefully Sirte, adding that others could still flee across the land border to Tunisia.
"We have 400 from Misrata, we have 300 from Benghazi and we have something like a couple of hundred from Sirte but the boat cannot go into Sirte because it's a shallow harbour so we need a small vessel to bring the people back out to the boat," he said.
He said the ship, chartered for about $1.8 million which can carry 1,500 passengers, would reach Libya at the end of the week
"We are counting on getting as many people as possible," so they can be brought to safety in Malta, he said.
An estimated 13,000 Filipinos were working in Libya when fighting between militia groups prompted the government in July to call for their "mandatory evacuation".
Despite repeated calls to leave, about 11,000 Filipinos are estimated to still be in Libya even as the violence shut down the airport and endangered road travel out of the country.
Del Rosario said the land route between Tripoli and Tunisia was now safe and would be used to evacuate people from the Libyan capital.
Some companies employing Filipinos were also evacuating them on their own, he said.
Philippine officials have said Filipinos were delaying their evacuation because they were more worried about not finding jobs at home.
About 10 million Filipinos work around the world, earning more money in a wide range of skilled and unskilled sectors than they could in their impoverished homeland.