Updated Wednesday 12.10am

Migrants who have spent the past three days aboard a ship built to house animals were brought to Malta late on Tuesday night.

Sources said that the roughly 50 people aboard the MV Talia were transferred to an Armed Forces of Malta vessel. They were brought to shore at around midnight. 

A video clip shared by NGO rescue hotline Alarm Phone at roughly 11.30pm showed people being transferred from a large ship to an AFM vessel. 

"Finally, after days kept in inhumane conditions on a livestock carrier off Malta's coast, the people who called us when in distress at sea are allowed to reach land in Europe!" the NGO wrote. 

The MV Talia, which is designed to carry livestock, was asked to rescue the group on Saturday as it was sailing to Spain. 

It had just delivered animals to Libya a few days earlier, and stables used to house them had not yet been cleaned when the migrants came aboard. 

Captain Mohammad Shaaban said that the rescue operation lasted four to five hours and the ship then proceeded to Lampedusa.

But Italian authorities refused disembarkation and Malta subsequently told the ship that it was not allowed to enter Maltese territorial waters. 

As rough seas picked up, the migrants were forced to move from the deck down into the soiled stables.

The captain has been calling for the EU, Italian or Maltese authorities to come to the migrants' aid.

A group of 35 non-governmental organisations on Tuesday also called on Malta not to abdicate responsibility for people on its territory and for whom it was clearly responsible.