The Global Fund to Fight Aids, TB and Malaria will make no new grants until 2014, and there is a threat to some existing projects.
It asked international donors for $20bn, but received just $11.5bn.
This misses even the fund's "minimum" $13bn target, which it says is needed to maintain programmes until 2014.
HIV charities said they were "extremely alarmed" by the decision.
This is the first time in its 10 year history that the fund has been forced to cancel its three-yearly funding round.
It blames the problem on a combination of "substantial budget challenges" in some of the countries who would normally contribute, and low interest rates cutting returns on its investments.'Worst possible time'
However, in recent years it has faced accusations of failing to make sure money reached those in need, commissioning a review in March after reports of "grave misuse of funds" in four recipient countries.
This led to some donors, including Germany and Sweden, holding back their funding temporarily.The HIV/Aids Alliance, whose member organisations rely heavily on the fund for projects across the world, said that it was the worst possible time for money to be withdrawn.
It said that planned projects to tackle high rates of HIV in areas of China and South Sudan might be affected by the funding cut.
Alvaro Bermejo, its director, said: "These should be exciting times - the latest scientific developments are showing us that HIV treatment can have a powerful HIV prevention effect.
"Never again must we reach a position where life-saving programmes are cancelled or delayed."
Another medical charity, Médecins Sans Frontières, described the financial situation as "dire".
He said that some countries with low HIV treatment coverage, such as Kenya, Lesotho and South Africa, had already been refused funding for larger scale programmes.
Dr Tido von Schoen-Angerer, one of its executive directors, said: "Donors are really pulling the rug out from under people living with HIV/Aids at precisely the time when we need to move full steam ahead and get life-saving treatment to more people."
He called for other governments to help make up some of the shortfall in donations.
The fund, which is based in Geneva, said that only "essential" programmes in low or middle-income countries would receive more funding to keep them going until 2014.
It says it intends to bring in new management to improve administration.