Ismaila Mamza, the emir of Uba, and Idriss Timta, the emir of Gwoza, were abducted at about 9 a.m. in the sect's stronghold, the north-eastern state of Borno, Xinhua reported.
Zhur, from where they were abducted, is located in the southern part of Borno.
The traditional rulers were said to be on their way to neighbouring Gombe to attend the burial of the late emir of Gombe.
A resident of Uba, Ezekiel Buba, told Xinhua in Maiduguri, the state capital, that the community has been informed about the kidnapping of their ruler.
However, a security source said military troops have succeeded in locating the emir of Uba, adding that "efforts were ongoing to secure his release".
However, there was no official confirmation from the military and state government on the abductions.