The veteran president, who has been the target of several coup attempts, said the vessels would safeguard the state and the Gulf of Guinea, the scene of pirate and rebel attacks.
“Equipping our navy such top-class vessels is not an ostentatious display or show, but a way of guaranteeing the security of our territorial waters,” he said during a naming ceremony in the capital Malabo.
The two missile-carrying vessels built in Israel span 72m and have a 470-ton capacity, state television reported.
The cost of the gunboats, named after the provinces Littoral and Kie Ntem, is not known.
Equatorial Guinea has been provoked in the past, where its waters have been invaded, the president said, referring to an attack by two armed men who arrived in Malabo by boat on 17 February 2009.
In August 2010 a military tribunal sentenced four Equatorial Guineans, who Amnesty International says were later executed. Malabo has never confirmed the executions took place.
The Gulf of Guinea has witnessed numerous attacks over the years by pirates and by rebels seeking a bigger cut of oil revenues.
“We cannot remain with our arms crossed… the security of Equatorial Guinea’s territorial waters has to be assured by our boats,” Obiang Nguema said.
Obiang Nguema came to power after his uncle Macias was toppled and then executed in August 1979. He presides over Africa’s third largest oil exporter, although poverty is nevertheless widespread among its 650 000 population.