Deaths among migrants crossing the Central Mediterranean have “skyrocketed” to more than 600 in the past four weeks as a consequence of Italy’s crackdown on NGO boats, two charities operating rescues claimed on Thursday.

A month after the Aquarius was turned away by Italy and Malta, leaving it stranded at sea with 630 migrants on board, the NGOs jointly operating the ship said political decisions in Europe had had “deadly consequences”.

Medicins Sans Frontières (MSF) and SOS Mediterranee said humanitarian operations were being “deliberately obstructed” and that NGOs were being prevented from saving the lives of people in danger of drowning.

The deaths or disappearances at sea of more than 600 people – among them many babies and young children – in the last four weeks alone represented more than half the migrant fatalities in the Central Mediterranean so far this year, the NGOs said. 

“Europe bears the responsibility of these deaths on its conscience," Sophie Beau, vice-president of SOS Mediterranee, said.

Italy’s stance on accepting migrant rescue boats operated by charities has hardened considerably since a coalition government was formed with the hard-Right League party calling many of the shots.

On Thursday an Italian coastguard vessel carrying 67 migrants rescued by a merchant vessel, the Vos Thelassa, docked in the Sicilian port of Trapani amid accusations that two men on board had made death threats against the crew. 

Matteo Salvini, Italy’s hardline interior minister of the League party, called the alleged aggressors “pirates” and “criminals” and said he wanted them led off the ship in handcuffs.

Opposition MPs called Mr Salvini heartless and said that the three women and six children on board should at least be allowed onto dry land.

Mr Salvini’s blocking of NGO rescue boats from Italian ports and his pledge to expel half a million unauthorised migrants living in Italy has gone down well with many voters, with support for his party almost doubling since the March election. 

His anti-immigration stance has sent shockwaves across Europe, with hardliners across the continent joining together to push for reform of asylum rules that has threatened once again the EU’s principles of freedom of movement.

On Thursday EU interior ministers agreed the bloc’s external borders must be protected at a meeting to discuss the migrant issue in the Austrian city of Innsbruck, but offered little in the way of concrete new proposals.

Austria withdrew a proposal for asylum cases to be evaluated outside the EU before the meeting in the face of stiff opposition from other countries and the European Commission.

EU leaders agreed at a crunch summit last month to consider "disembarkation platforms" for migrants most likely be located in north Africa – but several countries in the region, such as Morocco and Tunisia, have already said they will not host them.

MSF and SOS Mediterranee blamed the recent increased number of deaths in the Mediterranean on NGO boats being effectively pushed out of the Central Mediterranean area, where there have now been no charity rescue operations since late June.

Italy’s refusal to allow the Aquarius to dock forced the ship on a five-day voyage to the Spanish city of Valencia, and it is now in port in Marseilles while the NGOs assess the situation.

A second boat operated by the Spanish NGO Proactiva Open Arms docked in Barcelona with 60 migrants onboard last week after also being turned away by Italy. But it is unclear whether Spain – itself dealing with surging boat arrivals across the Gibraltar Strait from Morocco – will open its ports to more migrants from the Central Mediterranean.

Meanwhile the NGOs say that making such long trips with people often requiring medical attention is not sustainable. 

Italy and other European governments say the NGO operations have created a "calling effect" for migrants and been exploited by people traffickers. But MSF and SOS Mediterranee said the deaths over the last month showed that desperate people continued to flee violence, poverty and conflict regardless, and that rescue operations must be in place as the summer weather drew increased crossings.

“There has been a cold-blooded decision to leave men, women and children to drown in the Mediterranean Sea. This is outrageous and unacceptable,” said Karline Kleijer, MSF head of emergencies.