The comments by Ali Akbar Pour-Jamshidian follow recent health ministry reports about disease control challenges posed by uncontrolled border crossings.
Pour-Jamshidian confirmed that irregular migration complicates disease surveillance, particularly for TB, as migrants bypass medical screening.
While stating that repatriation of 2 million undocumented Afghans remains a priority, the official admitted lacking current deportation statistics.
He said Iran is installing smart surveillance systems, traffic cameras and violation tracking at borders to monitor crossings, especially for Arbaeen pilgrimage in Iraq in August.
Pour-Jamshidian announced plans to facilitate transit for legal pilgrims from Afghanistan, Pakistan and other neighbors during Arbaeen, when Iran serves as a transit route for pilgrims from the eastern neighbors to Iraq.
Iran hosts over 10 million Afghans, according to unofficial figures, which is a huge burden on the country’s resources.
According to official data, the TB rate among Afghans in Iran is reportedly three times higher than host communities.