The Malta Maritime Authority said it had received reports that the ship was boarded by men posing as police in Swedish waters on July 24, days before it entered the Dover Strait.
Officials said it was boarded by "eight to twelve persons allegedly masked and wearing uniforms bearing the word 'police' and armed with guns and pistols".
"During their stay on board, members of the crew were allegedly assaulted, tied, gagged and blindfolded and some were seriously injured."
The authority said the crew were reportedly subjected to "hard" questioning related to drug trafficking by those posing as police.
It said Swedish authorities on Wednesday told Maltese officials none of its law enforcement agencies were involved in the incident.
The ship, chartered by a Finnish company and carrying a cargo of timber, began its voyage at the Finnish port of Pietarsaari.
After passing through the Dover Strait its transponder, which electronically gives its position, appeared to have been switched off and only visual sightings were made afterwards.
The vessel's movements were last recorded on AisLive, a ship tracking system, off the coast of Brest, northern France, on July 30, although there are reports that it may have been spotted off the coast of Portugal more recently.
Officials at the London-based International Maritime Bureau, which works to combat maritime crime and malpractice, said they had no details about the ship's whereabouts, but could not rule out that it had been hijacked.
"The vessel could have illegally deviated, it could have been hijacked and pirates are taking it to another location, or it could be being used as a phantom ship, where it's identity is changed," said Cyrus Mody, an official at the IMB.
"If it has been hijacked, then ideally a hijack is for a ransom at the end of the day. We just have to wait to see if there is a ransom demand."
Other maritime experts cast doubt on whether the ship had been seized, saying it merely had not been heard from, which while uncommon, was not completely out of the ordinary.
"All that happened from our perspective is that it reported in to us on July 28 under mandatory reporting rules as the vessel enters the Dover Strait ... [and] we've had no interaction with the ship since and nor would we expect to," a spokeswoman for the British coastguard said.
Jeremy Harrison, director of communications at the UK's Chamber of Shipping, said: "This is speculation running wild.
"Why would you attack and seize a small-to-medium sized cargo ship carrying wood of all things?"