Lifeline said that one person had been evacuated for medical reasons and that general conditions onboard were worsening.
Malta’s offer resolved a stand-off with Rome, where a new government, co-led by the anti-immigrant League party, has announced it will no longer let in ships that rescue migrants.
The ships cover the sea route to Italy, where thousands of refugees have died in recent years.
Mission Lifeline, the aid group that runs the ship, welcomed Malta’s offer but said on Twitter that “we now need EU countries to welcome the people”.
Italy’s Prime Minister Giuseppe Conte said that his Maltese counterpart Joseph Muscat told him about his decision in a phone call.
The Lifeline has already spent five days stuck in international waters.
After reaching Malta, the migrants will be divided up among European Union members who are willing to take them in, Conte said.
He did not say when it would arrive.
“Italy will do its part and welcome a portion of the migrants who are on board Lifeline in the hope that other European countries do the same,” he said.
Conte said that the ship would then be impounded and its captain investigated over reports that he ignored instructions to let the Libyan coastguard pick up the migrants.
The Maltese government issued a statement opening up to the possibility of allowing the ship to dock, but not confirming it, and confirming possible legal action against its crew.
“In the event that the vessel enters Maltese ports, there shall be investigations and possible action taken in regards to the MV Lifeline,” it said.
An ad hoc agreement was being negotiated to distribute the migrants among willing EU countries, the statement said.
Four member states had already confirmed their participation and two more were considering it, the statement said.
It did not name the countries, but French President Emmanuel Macron later said France would be one of them.
At a news conference during a visit to Rome, Macron also welcomed the “sense of responsibility” shown by Muscat.
Immigration has become an urgent political issue across Europe in recent weeks, since the new government took power in Italy and German Prime Minister Angela Merkel’s ruling coalition split over the issue.
Europe took in more than 1mn migrants, mainly asylum-seekers from the Middle East and Africa, in 2015.
Since then, the numbers have fallen sharply.
One main route, from Turkey to Greece, was largely shut in 2016, and numbers have fallen to tens of thousands so far this year, a 77% decline on 2017, when almost 120,000 came to Italy.
However, the issue still sharply divides European governments and has led to a surge in anti-immigrant and far-right political movements across the continent.
Countries that have taken in large numbers of asylum-seekers want other European Union countries to share the burden.
Eastern European states, which have taken in some of the fewest, refuse to accept more and have turned the issue into a central focus for nationalist governments.
Leaders of the EU failed yesterday to come up with a joint position to tackle migration and will try again at a summit at the end of this week.
Also yesterday, Malta denied charity ship Aquarius access to its port for re-supply and a crew change, without providing any explanation for the decision, humanitarian group Doctors without Borders said on Twitter.
A private Danish cargo ship, the Alexander Maersk, carrying more than 100 rescued migrants and not covered by Italy’s ban on charity ships, was permitted to dock yesterday in the port of Pozzallo on the Italian island of Sicily.
