An American economist handed a key role at the heart of the EU directorate that oversees the regulation of US tech companies has quit hours after the French president, Emmanuel Macron, criticised her appointment as “dubious” and “extremely worrying”.

Fiona Scott Morton wrote to the EU antitrust chief, Margrethe Vestager, on Wednesday to tell her that she would not be taking the job because of the “political controversy”.

“Given the political controversy that has arisen because of the selection of a non-European to fill this position and the importance that the directorate general has the full backing of the European Union … I have determined that the best course of action is for me to withdraw and not take up the chief economist position,” she said in her letter, which was made public on Wednesday.

Vestager said she regretted the Yale University professor’s decision. “I accept this with regret and hope that she will continue to use her extraordinary skill-set to push for strong competition enforcement,” she tweeted.

In 2020, Scott Morton set out a roadmap for potential action to thwart Google’s dominance in the advertising market, which Vestager recently tackled in a landmark ruling that found Google had abused its monopoly in online advertising

She is considered one of the leading economists in the world in relation to industry and competition but her appointment last week immediately hit the headlines in Brussels given her previous role acting as a consultant for large US tech companies, including Apple and Amazon.

After a summit of EU and Latin American leaders in Brussels on Tuesday, Macron described the appointment as “dubious” and said the appointment of a foreign national to a similar role in the US administration would be blocked because of sovereign sensitivities. He also questioned how she could do her job “efficiently” if she had to recuse herself from decisions about companies she had previously advised.

In a swipe at Vestager, he suggested it was hard to believe that someone of the same calibre could not have been found in Europe.

Leaders of the main political groups at the European parliament had also chided Vestager for picking Scott Morton, who was chief economist at the antitrust division of the US Department of Justice during Barack Obama’s presidency.

Her appointment also prompted strong criticism from French politicians including the foreign minister, Catherine Colonna, who urged the EU to reconsider her appointment.

France’s Europe minister, Laurence Boone, one of the early critics of the appointment, told the Financial Times : “It’s not personal.” She said the concern centred on conflicts of interest in key roles that influence big businesses and there needed to be more transparency around any potential conflicts that might arise in such appointments.

“The rules on conflicts of interest during and after need to be clarified for these strategic positions,” she added.