Borrell triggered the row by saying he believed school students had been galvanised by teen Swedish climate activist Greta Thunberg without fully realising the costs they would have to bear to ensure a carbon-neutral future.
It “can be called 'Greta syndrome',” Borrell, 72, had said during a meeting at the European Parliament on Wednesday.
The Greens grouping of MEPs in the European Parliament criticised Borrell, tweeting that his comments “are unacceptable for a representative of the EU”.
On Saturday, Borrell said he had not meant to offend.
“I want to apologise to anyone that may have felt offended by my inappropriate reference to the important youth movement fighting #climatechange,” he tweeted in English.
The Commission has made tackling climate change the centrepiece of its action, pledging to spend billions of euros a year towards its Green Deal with the goal of making the EU climate change neutral by 2050.