A ministry spokesman said the group had been kidnapped in the desert zone near Lake Chad on the border with Chad.
"For the moment, we can say that they have been located but not freed," the spokesman told AFP.
However, a Niger government spokesman in Niamey said only two tourists had been abducted, and in the east of the country, not the southeast and that the search was being led by the defence and interior ministries.
"We can confirm that there was a kidnapping of two Italian tourists in a zone near the very porous (Chadian) border ... to the east of Agadez," said spokesman, Mohamed Ben Omar.
"The number (of tourists) is less than what has been given."
The Italian foreign ministry said there were not many more than 21 in the group and that the alarm was raised by a German tourist who managed to escape the kidnappers.
The Italian foreign ministry has not ruled out extortion as a motive.
It said in a statement that it has set up a crisis unit with Germany and is in contact with France, "the only European Union country that has diplomatic representation in Niger."
Italy is also in touch with contacts in Tripoli and Abidjan and is sending its charge d'affaires in the Ivory Coast, Giovanni Davoli, to Niger.
Mr Davoli has contacted Niger's interior minister to ask him to "do the maximum" to locate the tourists and find a "rapid solution without compromising their integrity in any way."