The two charities that operate the Aquarius migrant rescue ship in the Mediterranean have urged European governments to step in to secure its future after its Panamanian flag was revoked following alleged pressure from the Italian government.

Médecins Sans Frontières and SOS Méditerranée described the decision by the Panama Maritime Authority to deflag the vessel as “a major blow” to the ship’s humanitarian mission.

They claimed the PMA was forced to revoke the registration after coming under “blatant economic and political pressure from the Italian government”.

The charities are urging European governments to either call on the PMA to reconsider or issue a new flag to allow the Aquarius to continue its work.

The Aquarius is the last private rescue ship operating in the area used for crossings from Libya to Europe. It has been at the centre of a row about Europe’s approach to migration since Italy refused to allow it to dock on its shores in June. Last month it spent 19 days docked in the French port of Marseille after Gibraltar revoked its flag. It set sail again last week after first acquiring Panamanian recognition.

Italy’s anti-immigration interior minister, Matteo Salvini, has denied that his government was behind the decision to deflag the Aquarius. Writing on Twitter he claimed he did not know the telephone dialling code for Panama.

#Salvini: nessuna pressione su Panama per #Aquarius2, non so nemmeno che prefisso abbia Panama. #nonèlarena — Matteo Salvini (@matteosalvinimi) September 23, 2018

Mathilde Auvillain, a spokeswoman for SOSM, pointed out that for now the Aquarius could continue its work while at sea, but would need registration to allow it to dock.

Speaking to the Guardian she said: “We are asking EU governments to step up and provide the Aquarius with a solution. So far there have been no discussions with any government. At the moment we still have the Panama flag. We are still at sea involved in search and rescue operations. We cannot be deflagged at sea. We are still in shock at the announcement and assessing the situation and considering various options.”

She described Salvini’s denial as “strange”, pointing out that its announcement about the PMA’s decision did not mention Salvini.

In a letter to the ship’s operators the PMA said had it been urged to “immediate action” by the Italian authorities. SOSM and MSF quoted the PMA letter as saying: “Unfortunately, it is necessary that [the Aquarius] be excluded from our registry, because it implies a political problem against the Panamanian government and the Panamanian fleet that arrive to European port.”

Auvillain said the PMA did not go into details about the pressure it had received from Italy.

Karline Kleijer, MSF’s head of emergencies, said the fate of the boat highlighted the double standards of Europe’s politicians over migrants and refugees.

She said: “For the past two years, European leaders have claimed that people should not die at sea, but at the same time they have pursued dangerous and ill-informed policies that have brought the humanitarian crisis in the central Mediterranean and in Libya to new lows. This tragedy has to end, but that can only happen if EU governments allow the Aquarius and other search and rescue vessels to continue providing lifesaving assistance and bearing witness where it is so desperately needed.”

The French Socialist MEP Isabelle Thomas urged France’s president, Emmanuel Macron, to intervene by registering the Aquarius under a French flag. This would represent an “honour for our country”, she tweeted.