Iranian TV reported that some of the country's border police had been pursuing suspected drug dealers along the border, before following them into Pakistan where the suspects and guards were arrested.
Iranian police said that continuing to chase suspects who had fled into Pakistan was the normal procedure.
Relations between Iran and Pakistan have generally been good, but tension rose after Iran said last week's suicide bombing would affect relations.
Last week a senior Revolutionary Guards commander said his force should be given permission to confront terrorists inside Pakistan.
Mahmoud Ahmadinejad, Iran's president, said Jundollah operates from across the border in Pakistan, and urged Pakistan to hand over its leader, Abdolmalik Rigi.
Islamabad said it would help to find the perpetrators but denied the claim and that Rigi was in Pakistan.