The EU has congratulated former army chief Abdel-Fattah al-Sisi on his victory in the Egyptian presidential election and said it will “work closely” with the new government, days after documents seen exclusively by Middle East Eye revealed member states said the EU was “a puppet in the hands of the Egyptians”.

“The holding of the presidential elections marks an important step in the implementation of the constitutional roadmap towards the transition to democracy in Egypt,” said an EU statement released late Thursday. “The EU stands ready to support efforts by the new President and his government to take the necessary steps in the transition and to address the difficult economic situation in the country,” it added.

The EU said Sisi must tackle “serious challenges” facing the country, including “the deep divisions within society, the security situation, and the respect of the human rights of all Egyptian citizens”, and expressed concern at the “continued detention of members of peaceful civil society, political opposition and activists”.

Military-backed interim authorities have exacted a crackdown since a coup removed the country’s first freely elected president Mohammed Morsi from power last July. Over 1,400 people have been killed in clashes with police and more than 40,000 people have been detained for political reasons, with hundreds sentenced to death in short trials decried by human rights groups, according to Egyptian monitoring group Wikithawra.

Sisi won the 26-28 May election with 96.91 percent of the vote, although a lower than expected turnout of 47 percent led some commentators to question the level of popular support by the country’s next president.

The EU sent a team of monitors to observe the election, which led to a “difficult and critical” exchange between member states and representatives of foreign policy chief Catherine Ashton’s European External Action Service (EEAS), according to the internal minutes of a meeting held in Brussels on 19 May.

Fourteen out of 28 member states said a decision to reinstate the observation team, after it had been cancelled due to equipment being held by customs at Cairo airport, had undermined the EU’s credibility. The Netherlands said the EU was a “puppet in the hands of the Egyptians” and Ireland accused Ashton of having “given in to the Egyptians” by deciding to send monitors even though conditions fell short of international norms for observing elections.

Responding to reports that member states had criticised the decision to send monitors, a spokesperson for the EEAS said: “We do not comment publicly on internal EU discussions. We have several such meetings weekly.”

Sisi is due to be inaugurated as the president of Egypt on 8 June, with a national holiday announced for the occasion. Kings and heads of states are expected to attend the event at Cairo’s Ittihadiya palace.