Since shortly after the Israeli war on Gaza broke out in October, the Houthis have launched a spate of missile and drone attacks on Israel-linked ships in the Red Sea to pressure Israel to halt its ground invasion and allow unfettered aid access for Gaza.
The Houthis seized the Galaxy Leader on November 19.
"The information we have ... on the sailors of the Galaxy Leader captured in the Red Sea is that they are well, safe and sound," Transport Minister Georgy Gvozdeykov told private Bulgarian television station bTV.
The crew is staying at a hotel and their return to Bulgaria is being organised, Gvozdeykov added without providing further details.
The Galaxy Leader is owned by a British company, itself owned by an Israeli businessman.
It had been chartered by a Japanese company when it was seized by the Houthis, who said they were acting in "solidarity" with Palestinians trapped in the besieged Gaza Strip.
The fate of the 25 crew members -- who are Bulgarian, Filipino, Ukrainian and Mexican -- had not been made public until now.
In January, Bulgarian Prime Minister Nikolay Denkov said their release was the subject of discussions with the Houthis.
Negotiations are also underway over the bulk carrier MV Ruena, a Bulgarian ship sailing under Maltese flag which Somali pirates hijacked in December.
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