Migrants onboard the Open Arms charity rescue ship disembarked the vessel at the Italian island port of Lampedusa after the situation on board deteriorated on Tuesday.

An Italian prosecutor ordered the seizure of the Open Arms and the evacuation of the migrants after around 10 of them jumped off the ship, hoping to swim to the island, only a few hundred meters away.

Italy had refused to allow them to leave the ship for nearly three weeks, though dozens of children and the sick had been taken ashore.

Prior to the prosecutor's decision, the Spanish government said it would send a navy ship to Lampedusa to escort the Open Arms back to Spain.

The Open Arms ship, run by a Spanish charity of the same name, had rescued the migrants heading for Europe off the Libyan coast. The migrants were sleeping jammed together on deck and sharing two toilets.

Italian authorities ordered that the vessel be preventatively seized after inspecting the boat on Tuesday afternoon "given the difficult situation on board", a judicial source quoted by the AFP news agency said.

Open Arms' director and founder, Oscar Camps, confirmed on Twitter that the ship would be seized temporarily and welcomed the decision: "After 19 days, we will disembark today in Lampedusa.

"The ship will be seized temporarily, but it is a cost that Open Arms assumes to ensure that people on board can be seen to. We consider it essential to prioritize their health and safety in this humanitarian emergency."

Italy has taken a hard line on migrant entry, with Interior Minister Matteo Salvini leading a campaign that claims it has taken too much responsibility for coping with African migration to Europe.

Salvini suggested on Tuesday that the charity was exaggerating the problems on board. Of eight migrants taken ashore on Monday night for urgent medical attention, he said, only two had health problems.

"Being firm is the only way to stop Italy from becoming Europe's refugee camp again," he said on Twitter.

In a separate incident, Medecins Sans Frontieres (also known as MSF) reported that more than 100 migrants are thought to have drowned off the Libyan coast on Tuesday.

In a tweet, the organization said: "We have every reason to fear the worst — that over 100 lives were lost and nobody will ever know for sure."

These developments come as Italy's Prime Minister Giuseppe Conte resigned, leaving with a blistering attack on Salvini.

Conte said he was "irresponsible" in creating a new political crisis for "personal and party interests".

Salvini, the leader of the nationalist League party, had tabled a no-confidence motion against Conte. He also said he could no longer work with his coalition partner Five Star. Italian President Sergio Mattarella accepted the resignation and was due to consult party leaders on Wednesday.