The corporation ploughed an extra £61m into programming on its main channel BBC One to offset falling viewing figures, but ended up slipping from 25.2% of the audience share to 24.4%.
BBC Two lost even more viewers, slipping to 9.6% from 10.9% according to TV audience measurement body Barb, despite its programming budget being increased by £10m to £375m.
BBC Three was the only channel to have its budget cut, down by £6m to £93m, which is considered a sizeable amount of money considering BBC Three's audiences account for 0.48% of the overall viewing share.
In comparison, ITV lost more viewers than the BBC, but its digital channels, ITV2 and ITV3, performed better than the BBC's with ITV2's receiving a budget of £25m and garnering an audience share over 1%.
Overall losses at the BBC's digital channels are expected to amount to £188m, down from £250m in 2003 after the licence fee payment was increased above the rate of inflation to £126.50.
In total, the BBC made £2.94bn from licence fee payers, up £142m from the previous year.
The corporation will enter into Charter Renewal negotiations with the government this autumn. As it stands, the BBC has only secured a promise that it will be funded by the government for the next 12 years.
In addition, the annual report, due out on Tuesday, is expected to announce that £62m is to be ploughed into restructuring the BBC after director-general Mark Thompson's cull where 3,750 staff are expected to lose their jobs.
The restructure is part of Thomson's £355m cost-saving plan to be implemented over the next three years.
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