Maltese transport authorities had granted an NGO rescue vessel permission to leave local waters in August but the decision was reversed following orders from higher up, German NGO Sea-Watch has alleged.

In a statement issued on Tuesday, Sea-Watch lashed out at the Maltese government for the way in which it had communicated with the NGO throughout summer and accused Prime Minister Joseph Muscat of having given them “false hope”.

It said it was holding Dr Muscat responsible for deaths at sea which would could have been prevented had rescue vessels been free to do their work.

“For every preventable death that occurs at sea, your government has direct responsibility, which it shall acknowledge and rectify. It is time Maltese decision makers at highest levels, including you, are held to account for their deadly decisions,” Sea-Watch said.

The Sea-Watch 3 has been denied permission to leave Maltese ports for more than two months, with local authorities saying the vessel’s registration is not in order. Investigators from the ship’s flag state, the Netherlands, examined the ship and its documentation and said they see no problem with it.

The NGO said it had learned that its vessel was blocked through a government-issued press released and said that its requests to leave the island were denied “in an undocumented and vague form”.

READ: NGOs slam Delia's 'disgusting' anti-migrant comments 

It added that the Transport Ministry had decided to let the ship go at the end of August, on the condition that it would subsequently steer clear of Maltese waters. But that decision was reversed just a few days later, the NGO claims, “based on an alleged veto imposed at the highest government level”.

Last week, Sea-Watch announced that it had filed a judicial protest in an attempt to have a rescue plane that has also been blocked in Malta released, with the NGO having repeatedly said that the decision to ground it is based on cynical politics and not any genuine concern about its registration.