Independent music labels say Apple will not feature their artists on its European iTunes download service.
ITunes has been expanded to the UK, France and Germany
ITunes launched in parts of Europe on Tuesday, offering songs for 79p.
But the Association of Independent Music says negotiations between Apple and a number of its members have broken down because of differences over terms.
Some labels do not want to be locked into a deal that cannot be changed for three years and are angry Apple started negotiations so late.
Simon Wheeler, head of new media at the Beggar's group - whose labels have signed bands such as the White Stripes, Basement Jaxx and the Pixies - said they had not been able to agree a deal with Apple.
He told BBC News Online: "As far as I'm aware most of the key UK independents are not going to be part of the launch.
"It is the general terms. They came in very late in the day. We are being dictated what the terms will be for the next three years of a very young business.
"Apple are launching a very aggressive price. While it is below every other deal we have negotiated for some time, it is the locked-in factor that we have a problem with."
But Apple does not believe it has done anything wrong and is optimistic it will sign up the bigger independent labels.
Apple's vice president of applications, Eddy Cue, said: "We have signed dozens of independent labels in the UK but we want to sign more.
"Independent labels have been very successful in the US and they are very keen to have their music sold on the most popular online music store in the world."
Apple's competitors seized on the independents' disgruntlement.
Richard Ayers, editor of Tiscali.co.uk, said: "Online is a fantastic way for new bands to get exposure, but music downloading services should be supporting independent labels and new acts, not mugging them."
Russell Cook, label manager of another UK download service, Wippit, said independent music enjoyed a unique status in the UK.
"The UK and European markets are very different from the US. More than 25% of music sold here is independent.
"In essence, the UK has six major labels, not five and the indie segment is one of the biggest."
Mark Mulligan, a media analyst for Jupiter Research, said the lack of big independent music on iTunes was not a "body blow" for the service.
But he added: "It is unfortunate not to have strong independent music on board, especially in countries like France and Germany where domestic repertoire is so crucial.
"It's a problem that will need to be addressed by Apple."