Emmanuel Macron’s government has said “a political game” brought down France’s choice for European commissioner following an overwhelming rejection of the candidate by MEPs.

In a vote that spells trouble for the incoming European commission president, Ursula von der Leyen, MEPs emphatically rejected the French commissioner candidate, former MEP and defence minister Sylvie Goulard.

The centrist politician, who had been offered the high-profile job of leading the EU’s internal market policy, was voted down after a difficult encounter with MEPs on Thursday. At a second hearing with MEPs, Goulard expressed regret for a lucrative job she held with a US thinktank while she was an MEP.

An Élysée official said Goulard’s competence and European commitment had been recognised by all, but she had been “the object of a political game that affects the commission as a whole”.

Macron later insisted he was “very relaxed” as what mattered to him was the portfolio France would get at the commission. “I need to understand what has been in play. Resentment, perhaps pettiness. But I need to understand.”

Goulard was an early supporter of Macron in the European parliament after the upstart presidential candidate formed La République En March bidding to break the stranglehold of the established centre-right and centre-left. She became his defence minister but resigned after a month when a magistrate launched a preliminary investigation into allegations her party misused European parliament funds.

Nominated as France’s EU commissioner, she faced hostile questions from MEPs over those allegations and her work for the Los Angeles-based Berggruen Institute from October 2013 to the end of 2015, when she was paid more than €10,000 a month while working as an MEP.

On Thursday, she said she deserved the presumption of innocence over the allegations, which have never been tested in court. But she voiced regret for the thinktank job which she said had cast a doubt over her integrity and independence, values that she said were of “the utmost importance” to her.

Goulard’s vulnerabilities were heightened because MEPs have already rejected a centre-right commissioner candidate (from Hungary), as well as a socialist (a Romanian), meaning the parliament’s two biggest groups were looking for the weak points in her liberal group.

Some in the parliament suggested the outcome was “Weber’s revenge”, as Macron had crushed the hopes of Manfred Weber, a German centre-right MEP leader who aspired to lead the European commission but who was blocked by the French president.

In a statement, the liberal group (Renew Europe) said it deeply regretted the vote against “an excellent, skilled and committed pro-European commissioner” adding that she had “paid the price of European and domestic petty politics over an objective assessment of the commissioner candidates”.

The defeat is likely to trigger recriminations in the group over how they managed to lose Goulard in such a decisive way: 82 of the 112 MEPs eligible to vote on her appointment voted against her.

Goulard’s critics said the case showed the problems with the current system for assessing conflicts of interests.

“We obviously did not vote for Goulard,” said Manon Aubry of the radical left Unbowed France party. “EU citizens won’t put their trust in their institutions when a commissioner sees absolutely no problem in making €10,000 a month from a private lobby in addition to her MEP salary.”

The debacle has raised questions about whether the current European commission president, Jean-Claude Juncker, will be asked to extend his mandate beyond 1 November.

Von der Leyen, nominated as his successor in July, can only assume office following a positive vote in favour of her 26 commissioners. She now has three gaps, with neither a French nor a Romanian candidate. (Hungary proposed a career diplomat, Olivér Varhélyi, after Lázsló Trócsányi was rejected over an alleged conflict of interest, but the new nominee has yet to clear the parliament).

Following the vote, Von der Leyen met MEP group leaders and the European parliament president. “With so much at stake, it is now necessary, together with parliament, to speed up the process so that Europe can act swiftly,” she said in a statement that referred to the tasks of the next five years, including Brexit, climate change, trade, migration and digitalisation. “At the same time, all involved in the process need sufficient time to approach the next steps with care.”