London's High Court will hear the claim The Beatles' company Apple Corps Ltd discovered the shortfall during an audit. Legal proceedings were also filed at New York's Supreme Court.
Apple Corps chief NEIL ASPINALL says, "We have tried to reach settlement through good faith negotiations and regret that our efforts have been in vain.
"Despite very clear provisions in our contracts, 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."
Apple last took action against the label in 1991 when they successfully stopped EMI from releasing a Beatles album box set.
The last legal battle between the Fab Four and their record company occurred in 1991, when Apple won a High Court ruling preventing EMI from releasing an album box set on CD.