The man, stationed at the Foreign Ministry in Stockholm, was stopped when he and his wife were returning home after a charter holiday.
The diplomat had a marble rock stowed away in his luggage.
The "10 centimetre marble stone" was an ancient relic, and the man is now suspected of having tried to smuggle it out of the country, reported national newspaper Expressen.
According to the diplomat's wife, nobody had informed the couple that bringing these rocks home was forbidden.
"This is ludicrous. We had no idea that you couldn't take stones home as souvenirs," the woman told the paper.
"We don't know now what will happen, or how long we'll have to wait for a decision, but this is a mistake."
The Foreign Ministry has confirmed that the man is apprehended, and staff from the consulate in Istanbul has been to visit the man.
“We haven't heard any official criminal offense yet,” said the ministry's press secretary Catarina Axelsson to news agency TT.
However, Expressen revealed that a source had informed that the Turkish authorities take these kind of crimes "extremely seriously".