Briefing the National Assembly's health committee, she said the fund's "kitty is empty".
In April last year, the fund approved allocations of US616-million to about 40 countries, but at that stage it only had US347-million available to disperse -- leaving a shortfall of about 50 percent.
On January 15 this year, US2,2-billion had been pledged to the fund, but it only had US724-million readily available.
Tshabalala-Msimang discounted suggestions by committee members that the fund might be a "non-starter", saying she was hopeful that the developed countries would honour their pledges.
"We have got to rely on the goodwill of the developed countries and hope they will honour their pledges. We can only appeal, as I do all the time, for the pledges to be honoured," she said.
She was unaware of the reasons for the delayed pledge payments.
It was estimated that the fund needed about US2,5-billion to fund programmes this year, and about US3,8-billion in 2004.
Last year the fund approved several applications from South Africa for programme funding of about US21-million, including proposals by Lovelife, Soul City, the Lebombo Spatial Initiative and the national health department.
The controversial proposal by KwaZulu-Natal's Enhancing Care Initiative -- for US11-million -- which had not been submitted via South Africa's Country Co-ordinating Mechanism (CCM) as required by the Global Fund, had now been resubmitted "with modifications".
Tshabalala-Msimang said the changes had been agreed upon by her department and the KwaZulu-Natal initiative, and she believed it would be approved by the fund's board when it met in June this year, as it now had the CCM's backing.
Although several programme proposals had been approved, no money had actually been received yet. It was hoped the agreements allowing the transfers to be made would be signed in April, she said.
The global fund, which is solely a funding instrument and not an implementing agency, invites proposals for funding, which are then evaluated by an independent technical review panel, taking into account a number of factors.
These include that the proposal must build on and complement existing national and regional programmes.
Although all applications have to be made through a country's CCM, exceptions are made in cases where there is no legitimate government and ongoing conflict.
Applications are then approved or rejected by the fund's 18-member board, which has a rotating chairmanship.
Donor countries have seven seats on the board (France, Italy, Japan, Sweden, Britain, the United States, and a European Union representative) and developing countries also have seven (Brazil, Ukraine, China, Pakistan, Uganda, Nigeria, and Thailand). South Africa is an alternate member of the board.
There are also two seats each for NGOs and private sector donors - Sapa.