The report reveals that the value of the trust's investments fell by more than £100 million over the past year, which offset significant rises in revenue from membership dues, admission fees and legacies.
Reserves fell by £4 million during the year and now stand at less than a quarter of the target level of £42 million, or three months' income, set by the trust's governing council.
Director-general Fiona Reynolds said: "Like most charities, we are operating in a challenging financial climate, and the new financial year will be demanding on our resources.
"The value of what we do is clear to millions of people, however, and public support for our work has never been greater."
As well as investment losses, the charity has been hit by high spending on properties and a doubling of its contribution to its final salary pension scheme to £5 million.
Laurie Magnus, chair of the trust's finance committee, said: "The committee is currently working with the management board to establish a set of financial targets within which the trust needs to operate over the medium term to ensure that it generates a reasonable, but realistic, operating surplus. This will necessitate yet more focus on income generation and tight cost control."
The value of the trust's investments now stands at £562 million, compared with £673 million in March last year, following the 15 per cent loss over the past year. Investment income also fell by 15 per cent during the financial year from £25.8 million to £22.1 million.
Trust spokesman Julian Lloyd said: "Our curatorial work is intrinsically expensive and we will continue to be discriminating about the type of projects we take on."
The RSPCA is planning to shed 200 jobs after its reserves fell to £34 million, but Lloyd insisted the trust did not have any redundancy plans.
He said that getting reserves up to planned levels was a priority. "Income growth has been tremendously strong. If not we wouldn't be as confident as we are," he added.
The trust generated an operating surplus of £5.2 million: subscription income rose by 13 per cent to £75.6 million; income from visitors was up by 27 per cent to £10.7 million and legacies rose from £39 million in 2001/2 to £45 million by March this year.
The charity's trading arm, National Trust Enterprises, which comprises retailing, catering, camp sites and holiday cottage rentals, underwent strong growth, increasing its contribution to the trust by 30 per cent to £11.5 million.