The exact numbers are unclear, but Afghans are reportedly being transferred to camps. Some have been released -- but many others have been deported.
Several have called Radio Free Afghanistan to expresses concern over the situation.
"I am calling from Kerman. They have intensified their operations throughout Kerman province in recent days. [Afghans] are suffering," one Afghan man said. "They are collecting Afghans randomly; people with refugee IDs or without face the same treatment. They themselves issued ID cards for Afghan refugees -- why are they not paying any respect to these IDs? Why are they exposing people to suffering? The Iranian authorities are not giving us any direct answer about our neither, nor are Afghan authorities in Iran helping us."
Another caller said Afghans in Sirjan have been beaten up and forced to pay bribes.
Afghans have also been reportedly arrested in other cities, such as Mashad, which is home to a large Afghan community.
Xavier Creash is a spokesman in the office of the United Nations High Commissioner For Refugees (UNHCR) in Tehran. He says the refugee agency is monitoring the situation.
"Our people, our staff on the ground in the various cities concerned are trying to make sure that among these illegal migrants there are not registered refugees and if they find some registered refugees they immediately intervene. It has happened so far for very few cases," Creash said.
Iran denies that it has arrested refugees from Afghanistan, which shares a long border as well as cultural traditions with Iran. Dari, one of Afghanistan's main languages, is very close to Persian.
Ahmad Husseini is the director of Iran's Bureau for Aliens and Foreign Immigration Affairs. He has been quoted as saying that the claims are in contrast with official Iranian policies toward refugees.
Iranian officials say they have generously hosted more than 2 million Afghan refugees for two decades without receiving any significant international aid.
But since the fall of the Taliban in late 2001, they say it's time for Afghans to go home. Iranian officials view Afghans as a financial burden on Iran's economy.
In April 2002, a tripartite agreement was signed between Iran, Afghanistan, and the UNHCR to encourage the voluntary repatriation of Afghan refugees. Since then more than 1 million Afghan refugees have returned home, including some 400,000 Afghans who have returned since last March.
Touriali Ghiassi is a senior official with the Afghan consulate in Mashad. He says Afghanistan's first direct presidential election had a positive impact on the return process.
"It was really a step toward stability and peace in Afghanistan and it created peace of mind. In all these years, especially since 2001, we had the biggest number of returnees in 2004. Recent political developments in Afghanistan and the reconstruction process had an impact," Ghiassi said.
But he warns that the recent wave of arrests may negatively affect the repatriation of Afghans from Iran.
"There was a natural course in the return process of some of the Afghans who are residing in Iran without documents. They would spontaneously and voluntarily sign up [for the repatriation program] and leave Iran under police control. But today we don't have [this trend] anymore, because when Afghans are being raided from cities, they are not ready to return, they need time. And those who want to return are scared, they don't sign up and they remain even more secretly hidden. They think: 'We will be sent to camps, what is going to happen to our belongings? What is going to happen to us? How long are we going to stay there?" Ghiassi said.
There are more than 1 million Afghan refugees and thousands of illegal Afghan migrants living in Iran.
Many came to Iran following the Soviet occupation of Afghanistan and the civil war. Others came after the Taliban came to power in 1995. Many Afghan laborers have also come to Iran in search of work.
(Sultan Sarwar from RFE/RL's Afghan Service contributed to this report.)