Secret decks for extra animals have been found in a livestock carrier that sank off the Romanian port of Midia in November drowning thousands of sheep, according to the company carrying out the massive salvage operation.

Only 180 sheep survived out of the 14,600 initially believed to have been onboard the Queen Hind, which was carrying them from Romania, the EU’s biggest exporter of the animal, to Saudi Arabia.

But the revelations about secret decks are likely to increase the death toll by several thousands, and raise fresh questions on whether overloading was to blame for the capsize.

The vessel was left on its side in the water as it sank not far from port, with sheep corpses piling up around it. Images of the tragedy made headlines worldwide and led to renewed calls by animal activists to impose a ban on live exports from Europe to non-EU countries, particularly the Middle East and north Africa.

The Romanian national daily Adevărul reported on Sunday that the firm that won the auction to bring the vessel to shore, Grup Servicii Petroliere (GSP Offshore), made its first attempt on Saturday but operations were halted after the crane’s cables were unable to bear the load.

Gabriel Comănescu, GSP’s president, was quoted by Adevărul as saying that “during the operation, the divers entered the water, [and] found additional decks. These additional decks also have animals on board”.

Comănescu added: “There are decks not included in the cargo plan, they are undeclared. It is the problem of the authorities to find out why they were loaded and why they were not included in the cargo plan. It’s a big question. There is a much larger load than over 14,000 sheep.”

Gabriel Paun, of Animals International, said the revelation “confirms our initial suspicion that the vessel capsized because of overloading”. He added: “We are outraged that this came out from the company bringing the vessel back to the shore and not from the Romanian government itself.”

Animals International said it will file complaints to the EU commission and the Romanian prosecutor’s anti-corruption department.

“[GSP] came with the right equipment last week and they tried to lift it up with a crane and bring it to the shore,” Paun said. “They had calculated that the ship was full of water and animals, so they were prepared to lift more [weight] but still the cables broke.”

He had been told that the head of the company had sent down divers to investigate, and discovered secret decks loaded with thousands of animals.

Brian da Cal, UK director at the animal welfare organisation Four Paws, said he feared that the death of thousands of sheep could have been avoided.

“The allegations regarding hidden decks on the ship are of huge concern and strengthens our calls for an outright ban of long-distance transports of live animals and a maximum of eight hours transportation duration. No matter how strict the rules may be and how tragic this accident is, mass deaths like this are becoming more common.”

He said Four Paws was able to rescue 254 sheep from the half-sunken ship but several died later of exhaustion and injuries – 180 survived and are now being kept in a location north of Bucharest.

Paun said: “We’re saying that Romanian authorities are not to be trusted because this vessel has been inspected by the Romanian government [and] they’ve missed the extra decks which were not in the cargo plan.”

Paun said Romania exports about 3 million sheep annually. European live animal exports rose from a value of $1bn (£800m) in 2000 to $3.3bn in 2018.

An official from the Romanian national veterinary and food safety authority, in comments carried by Adevărul, appeared to dismiss the allegations and said the vessel was heavier because “dead sheep do not have the same weight as the live ones”.

A border police spokesman also dismissed the story as speculation.

The Guardian has contacted MGM Marine Shipping, the management company behind the Queen Hind, for comment. The Romanian embassy was also approached.