Iranian Foreign Ministry spokesman Hamid-Reza Asefi said Baghdad had "unfortunately and without warning" changed the terms of a long-standing arrangement, the official Irna news agency reported. He described Iraq's actions as "unacceptable".
Iranian reports said nearly 600 pilgrims on their way to a shrine in Karbala in southern Iraq were stopped at the Khosravi crossing on Sunday after Iraqi border guards demanded higher fees than agreed.
Iranian Foreign Ministry spokesman Hamid-Reza Asefi said Baghdad had "unfortunately and without warning" changed the terms of a long-standing arrangement, the official Irna news agency reported.
He described Iraq's actions as "unacceptable".
Iran says the agreement governing pilgrim crossings between the two countries - which sets out the level of entry fees - is not due to expire until late September.
Delays
Most of those stranded at the checkpoint are relatives of people who died in the two countries' brutal 1980-88 war.
They had gathered from across Iran to make the journey to the tomb of the Prophet's grandson, Hussein, in Karbala, but are now waiting in the border town of Qasr-e Shirin.
The town's governor, Mr Zakeri, said this was the third time such an incident had taken place.
"The first time this happened there was a one-year delay. The second time, there was a delay of a few days.
"Unfortunately, this sort of thing happens every so often," he said.