A total of 2,107 people sought medical treatment at hospitals and medical centres across five cities in Sistan and Baluchestan province due to recent dust storms, Majid Mohebi, the director general of the provincial Crisis Management Office, told state news agency Irna on Sunday.
More than 130 people remain in hospital and respiratory, heart and eye conditions have been "major problems", he said.
Dust storms, a frequent occurrence in Iran, have "increased dramatically" in the past two decades, researchers say.
The storms can also badly affect agriculture and infrastructure.
Three people have died in recent dust storms that have swept across the country's south-east, with the deaths attributed to "reduced visibility", Mr Mohebi said.
Aside from respiratory issues, the storms can also cause strokes and forms of meningitis as a result of bad air quality, studies have shown.
Researchers in the UAE have warned of potentially "disastrous" effects on human health as climate change creates more dust storms across the Middle East.
Authorities are on standby to help motorists with reduced vision due to the dust, Mr Mohebi said.
Schools and offices in Sistan and Baluchestan were closed this weekend, the start of the academic year, due to the storms.
Last month, officials said at least 1,000 people had been taken to hospital due to due dust storms and high temperatures.
Iran is among countries most vulnerable to the effects of climate change.
Deforestation and drought have worsened the dust storms.
The Iran Meteorological Organisation estimates 97 per cent of the country faces issues with some level of drought.
Cities on the Caspian Sea were hit by heavy floods last week, with Astara seeing its heaviest rains in a century.
Almost 100 people were killed in flash floods that swept across the country last year, affecting 21 out of 31 provinces.