EU member states expressed “incomprehension” when the European Commission president, Ursula von der Leyen, rushed into a migration pact with Tunisia, it has been revealed. The concerns were raised in July both verbally and in writing, the EU’s chief diplomat responsible for foreign affairs, Josep Borrell, wrote in a letter dated 7 September that has been seen by the Guardian. “As you know … in July, several member states expressed their incomprehension regarding the commission’s unilateral action on the conclusion of this [memorandum of understanding] and concerns about some of its contents,” Borrell wrote in a letter to Olivér Várhelyi, the European commissioner for neighbouring countries. “After the foreign affairs council meeting on 20 July some member states referred these concerns by written procedure to you.” The pact, signed with Tunisia in July by Von der Leyen, the Italian prime minister, Giorgia Meloni, and the Dutch prime minister, Mark Rutte, was aimed at stemming migration to Europe from Tunisia, which had become one of the most popular routes for people smugglers working in Africa after Libya became too dangerous even for organised criminal gangs. The letter also says that foreign affairs ministers had “observed the proper steps of the adoption procedure had not been followed” by the commission and that therefore the memorandum of understanding could not be “considered a valid template for future agreements”. It is not clear why Borrell wrote the letter two months after the deal was signed, but it appears to be an attempt to ensure that a similar deal is not repeated with other north African countries without proper consultation with member states. His letter recalls a previous high-profile clash between the commission and member states in relation to a rushed deal with Switzerland on another matter. In a broadside against Meloni and Rutte, Borrell wrote that “the participation in the negotiation and the signing ceremony of a limited number of EU heads of government does not make up for the institutional balance between the council and the commission”. The letter was written days before Sunday’s visit by Von der Leyen and Meloni to Lampedusa, a small island off the coast of Sicily that the Italian leader says has been overwhelmed by arrivals from Tunisia. The deal was aimed at combating the criminal gangs running the smuggling operations and strengthening border controls and search and rescue operations. However, since it was signed the number of people crossing from Tunisia to Italy has gone up almost 70%, though experts have pointed out that poor weather in May meant a rise was inevitable in June and July when the seas were calmer. The pact was driven by Meloni, but, apart from the objection from Borrell, appeared to be backed by the rest of Europe, where migration is seen as a critical issue in elections, particularly those looming in Poland and the Netherlands. On Wednesday, a group of MEPs from the European parliament were refused entry to Tunisia, raising questions about the partnership and further doubts over the willingness of the Tunisian president, Kais Saied, to address concerns about a reduction in human rights and the independence of the judiciary on his watch. The £105m deal was also criticised last week by the charity Médecins Sans Frontières, which said it would make the bloc “directly complicit in the ongoing abuse and deaths of people trapped in the country”. No money has yet changed hands in Tunisia but the EU said over the weekend efforts to help police the border were under way including the refitting of 17 vessels for the Tunisian authorities for search and rescue operations.