The migrants, including a newborn baby and three pregnant women, were apprehended on Tuesday off the coast of the capital Malabo, according to state television.
Coming from West African countries such as Benin, Nigeria and Togo, the migrants are being held at Malabo’s central police station, dubbed Equatorial Guinea’s “Guantanamo”.
“The boat’s leader told us that they on their way to Gabon. We do not know if it is true,” a coastguard told state TV.
Authorities aim to send the migrants back to their home countries in the coming days, police said.
Gabon and Equatorial Guinea have had an influx of migrants at their land and sea borders over the last few years, attracted by the relatively strong economies of the two oil-producers.
The two countries have been reluctant to implement long-running plans to allow visa-free movement in six central African countries – an agreement finally ratified in October – as they feared they would be swamped by job-seekers from poorer members.