The European Union’s competition commissioner has said that its probe into Apple’s tax deals with Ireland would continue even if the company moved some of its $200bn overseas cash pile back to the US.

Apple’s stated intention to repatriate a substantial portion of its overseas cash could prove crucial as it tries to fend off the EU’s long-running investigation into its alleged sweetheart tax deals with the Irish government.

Support has been growing in Washington for proposals to overhaul the taxation of American companies’ overseas profits, with presidential candidates including Donald Trump advocating a one-off mandatory levy at a reduced rate to encourage executives to bring the money home.

However, on a visit to Washington last week, Margrethe Vestager, the EU competition commissioner overseeing a probe into Apple’s Irish tax arrangements, said that moving its offshore cash around now would change nothing.

“Whether or not Apple wants to repatriate part of their unrepatriated profits is purely up to Apple and is of no concern [to] our case work,” she told reporters after meetings with the Obama administration and lawmakers in the US capital.

Apple’s accounts show that it has earmarked about half of its overseas cash for repatriation to the US. In October’s annual report, Apple estimated a deferred tax liability of $30bn related to a cumulative total of $91.5bn in foreign earnings. As a result, Apple’s advocates in Washington argue that European governments have no rights to those funds.

Ms Vestager travelled to Washington last week with tensions running high between the EU and the Obama administration. Jack Lew, the US Treasury secretary, had previously lashed out at the EU for conducting an unjust crusade against tax avoidance that singled out US companies.

The EU commissioner insisted that she was not targeting American businesses but indicated that her meetings with Mr Lew and senior senators had not resolved the fundamental points of disagreement. “I think it’s very much the same,” she said.

In a statement last week, a spokesperson for Mr Lew said that during their meeting, he had “expressed his concern that the European Commission is retroactively applying a sweeping new state aid theory with an outsized impact on US companies”, while noting that both sides of the Atlantic held a “shared objective of preventing the continued erosion of the corporate tax base”.

The scale of that alleged erosion is a matter of intense speculation. Asked about how much Apple may owe if the EU rules against Ireland, Ms Vestager said: “I have no magic numbers … The case is not done yet and therefore it is still very early days because only when we finalise our investigation will we know.”

With the probe now close to entering its third year, she blamed its apparently slow progress on the discovery of “new information” and said it was difficult to predict when it would be concluded.

Assessing the root cause of the heated debate between the two sides, she said: “Obviously it looks different from different sides of the Atlantic. We do something that we usually do, that we have done a number of times. And seen from here [in the US] it’s a novelty. It’s not seen in the US way of doing things.”

She added that having face-to-face meetings with her US counterparts was preferable to what the two sides had been doing: exchanging letters and waging war in the media. “One of the things that I would like to do is engage even more in order not to leave questions unanswered. We may disagree, but that shouldn’t be on the basis of things not being clear,” she said.