The label, backed by Netherlands-based fashion house Gucci, had already lost about £2.7m in the 2001-2002 fiscal year.
One third of the losses incurred in 2002-2003 were salary payments for 12 staff, including a £1.6m share for the highest-paid director, believed to be McCartney.
Gucci, which paid almost £6m to sign the label in 2001, has since contributed £8.94m to keep the Stella McCartney brand afloat.
However, the company is expected to continue to back the designer because of the significant investment involved.
McCartney, the daughter of ex-Beatles singer Sir Paul and a former designer for Chloe, also saw her label report annual sales of about £426,000.
Her designs were recently described as "amateurish" by noted UK designer Jeff Banks.