Appointed in 2009, Dastjerdi was the first woman government minister since the Islamic Republic was established in 1979. While seen as politically conservative, the gynaecologist has advocated a greater role for women in society.
Reports have emerged in recent weeks of shortages of some critical medicines for treatment of cancer, multiple sclerosis, blood disorders and other serious conditions.
Last month, Dastjerdi said only a quarter of the $2.4 billion earmarked for medicine imports had been provided in the current year and there was a shortage of foreign currency for the shipments.
"Medicine is more essential than bread. I have heard that luxury cars have been imported with subsidized dollars but I don't know what happened to the dollars that were supposed to be allocated for importing medicine," she said on state television.
Iranian officials blame the shortages on sanctions imposed by the United States and the European Union, but the government has come under heavy criticism itself for failing to manage the needs of Iranians properly.
Ahmadinejad's political rivals accuse him of exacerbating the effects of sanctions through poor management and cronyism.
In a short statement, he announced the interim appointment of Mohammad Hassan Tariqat Monfared as head of the ministry, replacing Dastjerdi.
"Noting your commitment and valuable experiences and based on the ... constitution, I appoint you as the caretaker health minister," read the statement published widely across Iranian media.