But hours later, the group reversed course, posting a second statement signed by a different leader that condemned the kidnapping and denied responsibility.
It was unclear if the contradictory statements indicated a rift in the Front for the Forces of Redress, or FFR, a group comprised of ethnic Tuaregs, a nomadic people who inhabit the vast deserts that cross northern Africa.
The second statement, signed by the president of the group, left open the possibility that dissident rebels acting in the name of the FFR could be responsible.
"If others who adhere to the ideals of the FFR did take the Canadian diplomat hostage, the FFR cannot assume responsibility," it said.
Ban Ki-moon, the UN secretary-general who appointed Fowler as UN special envoy to Niger in July, said his staff was doing all it could to find out what happened.
Fowler, his Canadian deputy and their driver were reported missing on Sunday after their abandoned car was found about 50km northeast of Niamey, Niger's capital.
The FFR is a splinter group in a larger rebellion being fought by Tuareg fighters in Niger's northern desert. The Tuaregs have long been at odds with the governments of the various states touched by the desert, including Niger.
A rebellion broke out in 1990 and ended with a 1995 peace accord. It promised a degree of autonomy, development funds for the north, and integration of the Tuareg minority into the country's armed forces and government.
But hostilities resumed last year as the government of Mamadou Tandja, the president, intensified uranium drilling in the northern desert.