Italian military officials have accused Matteo Salvini of “unprecedented interference” as tension mounts over the far-right interior minister’s policy of closing ports to rescued migrants.

Salvini, who is also Italy’s deputy prime minister, sent a letter to the heads of the navy and coastguard reportedly ordering them to maintain the policy by paying close attention to events at sea, in particular the movements of Mare Jonio, a charity rescue ship that was seized in March after defying an order not to bring migrants to Italy.

While the interior ministry oversees the police, which also received the letter, the navy and coastguard are within the remit of the defence ministry.

Sources from the military and defence ministries told the news agency Adnkronos that Salvini’s directive had “crossed a red line” and represented an “improper pressure”.

“The [directive] is a real and unprecedented interference in the recent history of the republic that violates every principle and protocol,” the sources said.

A group of MPs from leftwing parties have called for the issue to be raised in parliament.

“It is a question of government collegiality on very delicate subjects such as defence, foreign policy and the protection of borders – matters on which different lines cannot exist,” said Riccardo Magi, a politician with the Italian Radicals.

Salvini reportedly told navy and coastguard chiefs to watch the movements of Mare Jonio, a charity rescue ship. Photograph: Alkis Konstantinidis/Reuters

The row emerged after Fayez al-Sarraj, the prime minister of Libya’s UN-recognised government, warned fighting in the country could cause an estimated 800,000 migrants to flee to Europe.

Libya’s deputy prime minister, Ahmed Maiteeq, also warned 400 Islamic State terrorists held in prisons in the country could escape and try to reach Europe amid the chaos as the Khalifa Haftar, who rules eastern Libya, attempts to seize the capital, Tripoli. Maiteeq told reporters in Rome the fighting had so far killed more than 100 people and caused 18,000 to be displaced.

Salvini said the risk of terrorists infiltrating migrant boats was a “certainty” and he held authority in terms of public security.

“This is why I must reiterate that no docking will be allowed on Italian shores,” he told Rai Radio.

“The port is assigned by the interior minister, whether you like it or not, Italians pay me to defend them and I am doing it.”

Salvini closed ports to migrant rescue ships shortly after becoming interior minister last June, but the policy is causing friction with his government’s coalition partner, the Five Star Movement (M5S).

Salvini accused Elisabetta Trenta, M5S’s defence minister, of being “pro-immigration” after she criticised the policy, adding earlier this week that “with the war in Libya, migrants become refugees”. Salvini also dismissed comments by his co-deputy prime minister and M5S’s leader, Luigi Di Maio, who said the port blockade was “only temporary”.