Ursula von der Leyen’s run for a second term as president of the European Commission has been dented after accusations of favouritism in the selection of a fellow party member for a lucrative new job.

Some of the highest-ranking people in Brussels, including the EU’s chief diplomat, Josep Borrell, and the French commissioner Thierry Breton, have written to von der Leyen to complain that the appointment of the German MEP Markus Pieper as a special adviser “has triggered questions about the transparency and impartiality of the nomination process”.

Pieper, who comes from the same CDU party as von der Leyen, was appointed recently as special envoy for small and medium-sized enterprises, but MEPs have already questioned whether he was the highest-performing candidate in the selection process. According to reports, the job has a ranking within the commission that commands a salary of €17,000 (£14,580) a month.

The commission has defended the appointment saying it “has every confidence in the fact that the process took place in full compliance with procedures”.

The letter was also signed by Nicolas Schmit, the jobs and social rights commissioner, and Paolo Gentiloni, the commissioner for the economy.

The intervention of senior EU politicians in the controversy is the first sign of trouble for von der Leyen’s candidacy for a second five-year term at the helm of the commission. She was parachuted into the presidential candidacy process as a compromise candidate in 2019, so this is the first time she has had to run a campaign, which officially kicks off in Greece on Sunday.

Until now she had been considered a dead cert for the job. She had already been selected as the sole candidate for the job by the European People’s party (EPP), the umbrella group of EU centre-right parties to which the CDU party belongs and the largest group in the European parliament.

On Friday the EPP announced von der Leyen’s right-hand person in the commission, Björn Seibert, was taking unpaid leave to run her campaign. It said he would return to his job after the EU elections in June even though the campaign will not end until September, at the earliest, when the European parliament will be asked to vote on the new top jobs in Brussels.

Member states are expected to back her in a round of political horse-trading that follows the election and decides on the preferred candidates for the other principal roles, including chief diplomat and head of the European Council.

Her position is far from guaranteed, with the four signatories of the letter coming from non-EPP parties. Her reappointment after the EU elections will almost certainly need approval by those parties – Borrell’s group, the socialists, and Breton’s group, the liberals – to get a majority vote in September.

MEPs have already expressed concerns and tabled a written question to the commission asking how Pieper scored in the internal and external assessments.

The EurActiv website reported that the Czech MEP Martina Dlabajová and Sweden’s Anna Stellinger “both scored higher than Pieper in the assessments by at least 30%”, while Transparency International has called for an investigation into a potentially flawed appointment process.

In the letter, Breton and his colleague say: “Given that the response to the written question [by MEPs] is a matter for the commission as a whole, we consider it appropriate for the college to collectively discuss the answer to these allegations as well as the possible impact on the next steps in the recruitment process.”

In a sign of the political rivalries that are now at play before the elections, the commission spokesperson Eric Mamer pointed out that Breton was consulted over the process. He is widely seen as being close to the French president, Emmanuel Macron, whose party is aligned to the liberal group in the EU parliament, and has previously criticised von der Leyen, leading some to suggest he could yet emerge as a contender for her job.

Pieper did not respond to the claims but said he was “looking forward” to taking on the role, “even if it is with a heavy heart that I leave the parliament”. His allies said the controversy was “pure party politics” ahead of the election, pointing out that none of the signatories had raised objections before the appointment.