After a four year government investigation, General Electric Co. will pay a $50 million fine over its alleged misuse of hedge fund accounting which in one case, regulators said allowed GE to avoid missing analysts’ earnings expectations.

The Securities and Exchange Commission alleged in a federal court filing today that the industrial conglomerate, which also owns various media properties committed accounting fraud in 2002 and 2003.

GE settled the charges without admitting or denying the allegations, the SEC said. GE had received a notice in September last year that the SEC was considering taking court action.

“On four separate occasions in 2002 and 2003, however, high-level GE accounting executives or other finance personnel approved accounting which was not in compliance with Generally Accepted Accounting Principles (“GAAP”) so as to increase earnings or revenues or to avoid reporting negative financial results,” the SEC alleged in the complaint.

General Electric said today it settled the matter because “we have concluded that it is in the best interest of GE and its shareholders to resolve this matter and put it behind us on the basis announced today.”

“The errors at issue fell short of our standards,” GE said.

The conglomerate said it produced about 2.9 million pages of e-mails and other documents to the SEC and spent approximately $200 million in legal and accounting expenses to make sure issues were addressed appropriately.

The U.S. regulator said it took into account remedial acts by the company to improve its internal audit and controllership operations.