Claims that an EU decision to present Apple with a €13bn (£11bn) tax bill was designed as an attack on the US have been rejected by the European commissionpresident, Jean-Claude Juncker.

Last week’s ruling that the American tech giant must settle the massive tax bill with Ireland has gone down badly in Washington, with the US Treasury warning that the move risked damaging “the important spirit of economic partnership between the US and the EU”.

However, speaking on Sunday at the start of the G20 summit, in the Chinese city of Hangzhou, Juncker rejected the idea that European authorities were unjustly singling out US companies and said the ruling was “clearly based on facts”.

Commission investigations on taxation had mainly focused on European targets, he said, according to Reuters.

“This is not a decision against the United States of America,” Juncker told reporters. “It would be absurd to choose this territory of state taxation to attack the USA,” he added, according to AFP. “We are applying the rules … We are basing our decisions on facts and on the legislation.”

Both Apple and Ireland have said they will appeal against the EU ruling, which the Apple chief executive, Tim Cook, labelled “total political crap”.

“They just picked a number from I don’t know where,” Cook said after Tuesday’s announcement. “In the year that the commission says we paid that tax figure, we actually paid $400m. We believe that makes us the highest taxpayer in Ireland that year.”

Relations between Washington and Brussels have been tested by a series of anti-trust inquiries focusing on US technology firms such as Apple and Google thatsome have branded anti-American.

Speaking before President Barack Obama’s arrival in Hangzhou on Saturday, White House press secretary Josh Earnest said: “We need to find a way to make the global system of taxation more fair … [But] we also need to find a system that is fairer to companies who are looking to do business around the world. 

“And the US government is not going to hesitate to speak out in support of US companies that are looking to do business around the world. That’s good for the US economy, that’s good for US workers, but also benefits the international economy.”

The US wanted to ensure “that there aren’t entities or countries acting unilaterally in ways that exacerbate inequities in the global tax structure”, Earnest added.