Iran's National Organisation for Educational Testing has issued a list of university courses which prohibits Afghan refugees to study, a western news website reported.
The universities include Atomic physics, nuclear engineering, aerospace engineering, chemical engineering and military sciences.
The report also said that Afghan refugees are only allowed to apply at the universities in the areas where they live.
The prohibited areas included a dozen of provinces and many cities in different parts of Iran.
A spokesman for the Afghan embassy in Iran Mohammad Dehqani said that banned universities is not only for Afghan refugees but for all foreign nationals living in Iran.
"The Ban order is not only for Afghan refugees but it covers other foreign nationals too. Such limitations even exist in western countries, its not related to the political issues. As you know Iran has always supported education for Afghan refugees," Dehqani said.
Meanwhile, Nader Farhard, UNCHR commissioner believes that Iran should provide other facilities such as good living conditions, employment opportunities, education for kids and so on.
"According to UNCHR demands, if an area is declared prohibited, the legal refugees should have other options to live with honour and peace. They should have employment opportunities, their kids should be allowed to attend schools and should have access to other facilities,"
Mr Farhad said.
"We haven't witnessed forced deportation of any legal Afghans, but we are concerned about those 400 to 800 illegal Afghans expelled from Iran."
A Kabul university professor, Nasrullah Istanikzai, believes that as these universities are the main educational resources of Iran, they are not allowing Afghan and other countries' nationals to study.
"Because these universities are their main education treasures, they banned Afghan and other foreign nationals to study there. This proves that Iran is trying to enrich uranium," He added without elaborating.