Sir Paul McCartney and Ringo Starr are suing EMI over lost royalties allegedly worth $50million.
Apple Records - which is owned by Sir Paul, Ringo and relatives of the late Beatles members John Lennon and George Harrison - fought a previous court battle with EMI over royalties. That case was settled out of court in 1989.
The latest dispute claims an audit showed EMI - which owns the copyright to the Beatles recordings - has not been fulfilling the terms of its contract.
Legal proceedings have been issued in the High Court in London and the Supreme Court in New York.
Apple Records said in a statement: "Despite very clear provisions in our contract, EMI persist in ignoring their obligations and duty to account fairly and with transparency."
"Apple and The Beatles are, once again, left with no choice but to sue EMI."
An EMI spokeswoman said: "Artists do sometimes request an audit of their record label's accounts, that's not unusual, but sometimes there are differences of opinion, especially when the contracts are large and complex, when you can get issues of contractual interpretation."
"Ninety-nine out of 100 audit problems are resolved by amicable settlements for a small fraction of the claim."
