Last year, Malawians were urged to take an HIV test
Malawian civil servants with HIV, who used to receive an extra $35 a month to help them buy more food, are now to get a food handout instead.
"The money may not be spent on what you intended it for," Mary Shawa from the president's office told the BBC.
The new policy is part of a government review into its HIV policy and how best to fund it.
Malawi is among the countries worst affected by Aids, with about 7% of the 13m population affected.
The BBC's Raphael Tenthani in Blantyre says the government is the country's largest employer with about 120,000 civil servants.
Dr Shawa, responsible for HIV and nutrition in the president's office, said about 38,000 HIV mainly government employees will receive the food instead of the extra money in their pay packet.
"The recommendation is to give them cooking oil, some eggs as support," she said.
HIV-positive employees will also be educated about the virus and get advice about safe sex.
After years of silence, the authorities spoke out about the crisis in 2004, when a programme to tackle HIV/Aids was launched.
Dr Shawa said that is when free ARVs were introduced.
According to the UN World Health Organization, about 35% of those infected with HIV in Malawi are now taking ARV drugs.
Last year, the government called on all sexually active people in the country to take an Aids test.
The UN estimates that 80% of people with HIV in sub-Saharan Africa do not know they have the virus.