Ten Yemeni crew aboard the boat were dumped on shore, officials told Reuters.
"We understand that pirates hijacked the fishing vessel to hijack a big ship off the ocean," said Abdirahman Mohamud, head of maritime police forces in the semi-autonomous northern region of Puntland.
"They dropped its 10 Yemeni crew and a Somali guard inland and disappeared with the boat together with the food, cook, captain and engineer," he told Reuters.
Residents of Marrayo, a northern village near the pirate lair of Eyl, confirmed that pirates from their village had gone to hunt potential targets.
It is the second attack by pirates this month. On March 13, pirates seized a small oil tanker in the same region.
The pirates involved in Friday's attack are not seeking to hold the ship and its crew for ransom, but rather use the vessel as a "mothership", or launch pad for attacks on bigger ships.
"We're starting to see copycat attacks and there is a growing realisation that the shipping industry is taking huge risks," said John Steed, a former British defense attache who has worked on piracy for around a decade.
Those risks included sailing too close to the Somali coast becoming more relaxed about security needs.
In their heyday in 2011, Somali pirates launched 237 attacks off the coast of Somalia, data from the International Maritime Bureau showed, and held hundreds of hostages.
But attacks fell as shipping firms tightened security measures, such as posting lookouts, blocking easy entry points to the ship with barbed wire and installing secure panic rooms with communication equipment, known as "citadels".
Many ships hired private security and international warships also intensified patrols in the region.