Only around 435 HIV positive cases have been registered with authorities, "however it is estimated that there are 2,000-2,500 HIV positive cases nationwide," the ministry said in a statement.
The population of Afghanistan is estimated at 24-30 million people. The country has never done a full census.
"The prevalence of HIV in Afghanistan is currently considered low," the statement said.
But factors such as growing heroin injection, the low use of condoms, poverty and a high illiteracy rate put the destitute country at risk, it said.
The World Bank last month approved a 10-million-dollar grant to fund government efforts to keep the HIV/AIDS rate low.
The ministry said nearly four million dollars of this would be allocated to "harm reduction," including needle exchanges for intravenous drug users.