Migrants on a rescue boat which docked in an Italian port for the second time in a week despite an explicit government ban, have disembarked on the island of Lampedusa.

Humanitarian group Mediterranea Saving Humans, said the vessel was seized by police and its captain put under investigation for aiding illegal immigration.

More than 40 migrants on board were "finally allowed to disembark to receive assistance", it said on Twitter.

The boat was banned from docking by Italy's hardline interior minister Matteo Salvini, who issued a ministerial decree.

Italy's migration policy is deepening rifts in Europe as non-government organisations (NGOs) clash with Italian authorities over rules that effectively close off the country's ports to their boats.

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Italy's coalition government, which includes the right-wing League, blames European partners for leaving it alone to deal with sea arrivals.

New rules were adopted last month threatening NGO ships entering Italian waters without permission with a fine of up to 50,000 euros and the impounding of their vessels.

German interior minister Horst Seehofer on Saturday, asked his Italian counterpart Mr Salvini to rethink the ports shutdown.

The vessel "Alex" docked at the same quay where a week ago another charity vessel collided with an Italian police boat when its captain decided to bring migrants ashore after two weeks in international waters.

The German captain of the Sea-Watch 3 boat, 31-year-old Carola Rackete, was arrested in Lampedusa earlier this month before a Sicilian judge ordered her release a few days later.

The German interior minister said he was working with the European Commission to find solutions for people aboard the Alex and the Alan Kurdi, a second NGO ship which is close to Italian waters and has also been denied permission to enter.

In a tweet late the NGO Sea-eye said the Alan Kurdi had changed its course to Malta. It said it could not wait until the state of emergency prevailed.

"We cannot allow ships with rescued people on board to be left sailing the Mediterranean for weeks because they can't find a harbour," Mr Seehofer wrote in a letter. "We need swift European solutions in a spirit of common responsibility and solidarity."

But Mr Salvini replied in a Facebook video that a policy change was out of the question.

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"Dear German government, I'm not reopening the ports ... if anything we're going to put ... (the migrants) in a car and take them to the German embassy," he said.

"If someone is used to considering Italy a dumping site for all the problems Europe pretends not to see, that's over. And this applies to the French and the Dutch," he added,

He also called on fellow ministers to help more over migrants.

The Alex was escorted to Lampedusa by an Italian naval vessel and a sea patrol boat, but the migrants were not allowed to leave the boat and policemen stood on the quay.

"The migrants must be immediately disembarked and taken care of," tweeted MSH, which operates the Alex.

Italian tax police ordered the boat to be seized and its captain put under investigation for aiding illegal immigration, opening the way for the migrants to disembark.

MSH had declined a Maltese offer to go to the city of Valletta, saying the people aboard could not sustain such a long journey.

But Mr Salvini said Rome would not "yield to blackmail" and that armed forces were ready to intervene.

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"I'm not authorising people who ignore Italian laws and help human traffickers to disembark," he said on Twitter.

Meanwhile, MSH spokeswoman Alessandra Sciurba, said the charity had no choice but to head to the closest port due to health and hygiene conditions aboard the Alex.

Italy's interior ministry said it had provided food, medicines and 400 litres of water, while another 400 had been refused by the Alex due to a lack of space.

"They refused water so that they could declare the state of emergency ... we won't be intimidated," Mr Salvini said.

The League will propose increasing fines for NGOs violating the docking ban up to 1 million euros and making it easier to seize vessels, he added.