The latest clash came as BA submitted its response to the preliminary findings on the link-up from Karel Van Miert, the competition commissioner. They are understood to include a demand that the airlines give up around 350 take-off and landing slots at Heathrow Airport.
BA told the EC its conclusions had been "muddled" because officials had concentrated on single journeys between the UK and US, rather comparisons with passengers who used the airport to connect to other European destinations. BA has consistently argued that passengers on connecting flights from elsewhere in Europe have a wide choice of alternative routes to the US.
Mr Van Miert's spokesman denied that the EC's research had been flawed. "We think we've done our job very earnestly but we're not going to get into a verbal war over this. We are now going to scrutinise their figures."
But the EC gave the alliance a boost by confirming that it would complete its investigation well before November, when the two carriers would have to submit joint flight plans to the international regulator. Other watchdogs, the Office of Fair Trading in the UK and the US Department of Transportation, are also still considering the link-up.
The EC spokesman said the investigation was not running late. "We're on schedule, but we need to do our homework for legal reasons. We've always said we'll be ready before November."
The Commission's preliminary report concentrated on 17 routes where BA and American would have a virtual monopoly. The alliance, which would also control 60 per cent of all UK-US flights, would go beyond conventional code-sharing agreements between some carriers, with the pooling of ticketing revenues and marketing campaigns.
BA's submission yesterday admitted the two airlines would have a monopoly on 19 routes, though it said this was less than other alliances between European and US carriers. It stressed that the alliance would accompany an "open skies" agreement between the two governments, to liberalise access to Heathrow.
The link-up has attracted unprecedented hostility from rival US carriers. Delta Air Lines this week raised the stakes further by demanding that the two carriers give up as many as 800 slots at Heathrow.