Iranian police confirmed the incident without giving details of casualties, while local news agency Mehr reported one Iranian border guard had been killed.
Both sides blamed the other for shooting first.
"In the clash, one person was killed on each side and many were injured," tweeted the Taliban's interior ministry spokesman Abdul Nafy Takor about the incident in the southwestern province of Nimroz.
"The matter has been brought into the notice of the leaders on both sides and now the situation is under control. The Islamic Emirate does not want a war with its neighbor," the spokesman said, using the Taliban government's name for the country.
Iranian state news agency IRNA quoted the deputy head of the police force, Qassem Rezaee, as saying that "Taliban forces started shooting with all kinds of weapons" at an Iranian police station in Sistan-Baluchistan province.
Tasnim news agency reported that "light and semi-light weapons and artillery were used in the clashes".
Even though Tehran and Kabul are bound by diplomatic relations, the Islamic republic of Iran does not recognise Afghanistan's Kabul government, and ties between the two have been recently tense over a water dispute.
Last week, Iran demanded that Afghanistan respect its "water rights", charging that an upstream river dam there is restricting the flow into a lake that straddles their common border.
During a visit on May 18 to drought-parched southeastern Iran, President Ebrahim Raisi said: "I warn the rulers of Afghanistan to immediately give the people of Sistan-Baluchistan their water rights."
The Helmand River flows from the mountains of the central Afghan province of the same name for more than 1,000 kilometres (600 miles) into Lake Hamoun, which straddles the Afghanistan-Iran border.
Afghanistan has blamed climatic factors for reduced river volumes.
Iran maintains that the country's share was legally defined in a 1973 agreement between the two sides and demands that Taliban leaders uphold the deal, and last week it said Tehran "reserves" the right to take action to settle the dispute.
On the same day as the border clashes, Afghanistan's Foreign Minister Amir Khan Muttaqi met with the Iranian ambassador to Afghanistan Hassan Kazemi Qomi in Kabul where the two discussed "coordinated management of the border", the foreign ministry said in a statement.
"Assuring Iran's rights in the waters of Helmand river" was also discussed, it said.
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