"We have used all the vaccines we had," Health Ministry spokesman Adrian Chikumbe told AFP.
"The fact that there is only one cholera vaccine manufacturer worldwide makes it difficult to acquire the life-saving drug," said Chikumbe. "We are competing for the same vaccine with everyone else."
The southern African nation has been battling its worst cholera outbreak on record, with more than 30,600 people infected since the first cases were reported last year.
In November, it received almost 3 million doses of oral cholera vaccine from the United Nations to step up its immunization campaign, but case numbers continue to rise.
"What we need is high compliance to hygiene and sanitation," Chikumbe said.
George Jobe, director of the non-profit Malawi Health Equity Network, blamed myths and misinformation spreading online for the dire situation.
"Most people don't believe we have cholera," he told AFP.
Critics say the outbreak caught authorities off-guard when it hit almost 12 months ago.
Preventive health services chief Storm Kabuluzi said the government and aid groups were working to provide safe water and hand washing facilities. But he blamed some social sections for fueling the disease's spread.
"We have some religions that do not permit their members to go to the hospital," when ill, he said.
The death toll reached 1,002 on Tuesday, breaching a grim milestone and the previously recorded largest outbreak, which killed 968 people between 2001 and 2002, according to the World Health Organization (WHO).
Cholera, which causes diarrhea and vomiting, is contracted from a bacterium that is generally transmitted through contaminated food or water.