The Panamanian-flagged Whiskey Trio, belonging to a Turkish company called Trio Shipping, has remained at the Varberg port in Halland county since Friday.
Thomas Astrom, a senior official at the Swedish Transport Agency told AFP, "we are prohibiting them from leaving port, mainly for safety reasons, but also because of the working conditions for the crew."
The alert was raised by a seafarers' union after a Whiskey Trio crew member told it that he was not given permission to see a doctor despite being ill.
The transport authority, questioned by AFP, did not reveal the nature of the ship's cargo which was scheduled to leave for the Netherlands.
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The authorities did though speak of multiple breaches of safety rules, notably in the areas of fire safety and safety and rescue equipment.
The poor living conditions were also cited, including dirty and dilapidated cabins, outdated food and insufficient water points.
The Aftonbladet daily, without citing sources, said the ship was carrying explosives ultimately bound "for the Middle East.