Saudi diplomats in Iran have been seeking Iranian permission for Iman to leave the country.
"We were informed by the Saudi Arabian embassy ... some time ago that one of bin Laden's daughters is in the Saudi embassy in Tehran," Mottaki said on state television.
"We do not know how the individual ... entered the Saudi embassy and Iran in the first place. Her real identity is not yet clear to us.
"Upon determination of her real identity, she will be able to leave Iran with proper permits."
Mottaki made no reference to any other relatives of bin Laden living in Iran.
The Times reported on Thursday that the group included a wife and children who disappeared from bin Laden's Afghanistan camp at the time of the 9/11 attacks on the US in 2001.
It said other relatives found out last month that the group - including one of bin Laden's wives, six of his children and 11 of his grandchildren - had been kept in a high-security compound outside Tehran for the past eight years.
Abdul Rahman bin Laden, bin Laden's fourth son, had told Al Jazeera earlier this week that he had been unaware whether his relatives were alive until Iman contacted him a month ago. He then told her to go to the Saudi embassy.
He told Al Jazeera that he was concerned for his sister's health and he called on Tehran to release his relatives.
He also called for the Saudi government to ensure his sister's departure from the country.
The Times quoted Omar bin Laden, 29, who it said was Osama bin Laden's fourth-oldest son, as saying he had no idea that his brothers and sisters were still alive until they called him in November.
They told him how they had fled Afghanistan just before the 9/11 attacks and walked to the Iranian border. They were taken to a walled compound outside Tehran where guards said they were not allowed to leave "for their own safety".
Omar bin Laden said that his relatives lived as normal a life as possible, cooking meals, watching television and reading. They were allowed out only rarely for shopping trips.
"The Iranian government did not know what to do with this large group of people that nobody else wanted, so they just kept them safe. For that we owe them much gratitude, and thank Iran from the depth of our heart," he said.
He now hopes that the family will be given permission to leave Iran and join his mother, brother and two sisters in Syria, or himself and his wife in Qatar.
US soldiers and Afghan militia forces launched a large-scale assault on the Tora Bora mountains in 2001 in pursuit of Saudi-born bin Laden. Bin Laden has never been found and is believed to still be hiding in the mountainous border areas of Afghanistan and Pakistan.