After days of stand-off the passengers, who include children, will be taken into quarantine in Sicily.
The decision to allow the group to disembark follows a week of tension on board the ship
Italy has given permission for 180 migrants rescued from the Mediterranean to disembark from a charity-run ship.
The decision comes after a stand-off that lasted more than a week.
The Ocean Viking, operated by rescue group SOS Méditerranée, declared a state of emergency on Friday, citing fears for the safety of both migrants and crew.
The migrants are set to be transferred to a government vessel in Sicily on Monday and will quarantine for 14 days.
Medics have already tested those on the Ocean Viking for Covid-19. Results are expected on Monday.
The migrants are from a range of countries including Pakistan, Eritrea and Nigeria. They had fled the coast of Libya when they were rescued in four separate groups between 25 and 30 June.
They include 25 minors, most of whom are unaccompanied by adults and two women, including one who is pregnant.
The ship had been awaiting permission to allow the passengers off the vessel in either Italy or Malta.
As time went on, those on board had become desperate to reach land - while others, unable to contact friends and family to let them know they were safe, had become distraught, AFP news agency reports.
A doctor for SOS Méditerranée said he had noted "enormous psychological discomfort on the ship", where the situation was "almost out of control, for guests and crew".
One crew member said there had been a series of fights and threats of suicide.
An Italian interior ministry source told AFP that a medical team had been sent to the ship ahead of disembarkation.
"We're very happy! We've come a long way, Libya was like hell and now at least we can see the end. I need to tell my family that I'm still alive," said one passenger, 27-year-old Rabiul from Bangladesh.
SOS Méditerranée wrote on Twitter that the "unnecessary delay of this disembarkation has put lives at risk".
More than 110,000 migrants tried to cross the Mediterranean last year. More than 1,200 died during the attempt, according to the International Organisation for Migration.
It is thought that warmer weather during summer could lead to an increase in the number of attempts. BBC