The ministry’s spokeswoman Sima Sadat Lari told state TV that 458 people died from COVID-19 from Sunday to Monday, pushing the death toll to 38,749.
The spokeswoman said that of the new cases detected since Sunday, 3,574 patients have been admitted to the hospitals.
Among those undergoing treatment in medical centers at present, 5,561 coronavirus patients have critical health conditions, she noted.
At least 525,641 patients have recovered from the coronavirus infection so far or have been discharged from hospitals across Iran, the spokeswoman said.
Lari warned that all of Iran’s 31 provinces are currently recorded as red zones with high risk of coronavirus transmission.
Iran is struggling to contain the pandemic since February, when the first cases were confirmed in the city of Qom.
The government has imposed restrictions as the country battles a third wave of the virus.
It has closed schools, mosques, shops and restaurants in most of the country.
Authorities have said coronavirus tolls will spike again if Iranians fail to respect preventive measures such as social distancing and wearing face coverings in public.
On Saturday, President Hassan Rouhani outlined a new list of measures during a meeting of the National Headquarters for Managing and Fighting the Coronavirus.
Rouhani said under the new measures nonessential businesses such as malls, small retailers, cinemas and gyms would close from 6 pm for a month, starting Tuesday.
This would apply to the capital Tehran, provincial capitals and “cities with high populations,” he added.
The rising toll has brought a number of health experts and officials to call for a lockdown in the capital as a minimum measure.
Some hospitals have run out of beds to treat new patients, Nader Tavakkoli, a member of the National Headquarters for Managing and Fighting the Coronavirus told ISNA.
“Beds allocated for coronavirus patients are full at hospitals,” Tavakkoli said. “We should have a temporary phase of two weeks closure in Tehran to control the wave of the disease ... meanwhile we can get into planning.”
Iran has not imposed a full lockdown since it was hit by COVID-19 in February, with Rouhani arguing the country's sanctions-hit economy cannot afford to be shut down for an extended period.
Tasnim News Agency and Reuters contributed to this story.