The incident on Saturday night was the latest act of piracy in the Gulf of Guinea, which spans more than 5,700 kilometres (3,500 miles) from Senegal to Angola off Africa's west coast.
"This attack, perpetrated by three armed individuals, led to the abduction of nine crew members, including five Chinese nationals and four Indonesians," the navy's chief of staff Hubert Bekale Meyong said in a video statement broadcast by Gabonese media on Monday.
"The trawler IB Fish 7, flying the Gabonese flag, was the victim of a pirate attack while engaged in fishing about seven nautical miles southwest of Ekwata, in Gabonese waters," he added.
Six other sailors of Indonesian, Chinese and Burkinabe nationalities remained onboard the vessel, he said.
Gabonese authorities located the trawler before it was escorted to the port of Libreville and an inquiry has been opened.
In February last year, three sailors were kidnapped at gunpoint from a fishing trawler in waters near the capital.
Part of the Atlantic Ocean, the Gulf of Guinea is a key maritime route for oil and gas as it borders west Africa's major oil producers.
It is also popular with amateur fishing enthusiasts, pleasure-boaters and tourists keen to go whale watching off Gabon's coastline.
The waters were long considered among the most pirate-infested in the world.
But in recent years pirate attacks have become less frequent after a joint crackdown by countries bordering the gulf, alongside several European nations.
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