Brian Mawhinney, Secretary of State for Transport, told a meeting of ministers in Luxembourg that the commission did not have the legal power to negotiate a transatlantic aviation deal for Europe.
He said Britain would start talks with the US next week on a second new package to liberalise airline services.
As EU transport commissioner, Mr Kinnock has threatened Britain with legal action because he believes the move will harm Europe. Mr Mawhinney said defiantly that "that's a matter for Mr Kinnock".
Mr Kinnock wants the power to negotiate on behalf of all 15 member states with the US and is already taking legal action against six countries whichhave initiated bilateral deals with Washington.
Yesterday, the EU transport ministers asked Mr Kinnock to draw up a study by the end of the year on the benefits of a joint negotiating stance and the possible common interest. Only then can he get a mandate to negotiate - and talks between the 15 indicate it will not be easy.
Mr Mawhinney said there were much more fundamental problems. Asked whether he believed the commission had the legal competence to negotiate such an agreement, he answered "no".
A controversial legal case last year on commission powers to negotiate international deals had left the situation unclear. Mr Mawhinney said he thought another court case would be required - indicating he would relish a legal battle with Mr Kinnock.
Mr Kinnock said: "I don't believe there is any doubt about the commission's competence." But he agreed that "it may have to be resolved in court".
He said that only Britain spoke against the commission's powers, but Mr Mawhinney said several states had doubts.
Other countries were also concerned that any new negotiating mandate should not weaken what they had already agreed or might achieve, a commission official said.
"They want to ensure there is no roll-back," she added. "And they want to know the hows, the whys and the wherefores. That will require us to do more economic work."
The commission believes that bilateral deals will weaken airline liberalisation in Europe and harm some countries.
Legal proceedings against six countries that have already initialled deals (Austria, Belgium, Luxembourg, Denmark, Finland and Sweden) have already begun and a letter to Britain is imminent.
The commission official rejected the idea that Mr Kinnock was given the brush-off from transport ministers yesterday, saying: "This is as much as he would expect to have got at this stage of the proceedings."
Mr Kinnock said he was delighted at the results.Reuse content