The president thanked industry minister Mohammad Shariatmadari and roads minister Abbas Akhoundi's "selfless service" and "sincere efforts" during their tenures and appointed two acting ministers.
Reza Rahmani, current deputy industries minister, will take over for Shariatmadari and the current governor of Mazandaran, Mohammad Eslami, will become acting roads minister effective immediately, the website said.
The two ministers reportedly handed in their resignations over a month ago as lawmakers were preparing impeachment proceedings against them.
Rumours of Shariatmadari's resignation first surfaced mid-September but were quickly denied by the ministry.
Akhoundi published his resignation letter dated September 1 on Saturday, pointing to a "difference of opinion" as the main cause.
Rouhani's labour and economy ministers were sacked by the parliament in August over their handling of an economic crisis, partly triggered by the withdrawal of the United States from the 2015 nuclear deal and reimpoisition of sanctions.
Rouhani himself was summoned to the parliament to answer questions from lawmakers on August 28, a first in his five years in power, and only the second time for a sitting president.
Lawmakers were also ready to impeach education minister Mohammad Bathaei but called it off on September 2 due to the upcoming school year.
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