The message said Fowler was in good health and that the operation was a warning to "all diplomats who collaborate with the ethnic-killing regime of [Niger President] Mamadou Tandja".
The FFR split in May this year from the Niger Justice Movement (MNJ), which operates mainly in the desert north. The groups say the Tuareg people are being neglected and marginalised by the government.
The government is battling the MNJ in the north of the country, but the region where Fowler disappeared is well away from the area.
The vehicle used by Fowler was found about 40km from the capital, Niamey.
Mohamed Ben Omar, Niger's minister of communication, said that Fowler had been planning to attend celebrations marking the 50th anniversary of Niger gaining its autonomy from France and was not on official business.
"Without making a prior request for authorisation from the authorities," Fowler left the capital on Saturday with two other people, including a driver, the minister said.
He was apparently heading to Samira, the site of a gold mine that is part-Canadian owned.
Officials were told about his disappearance on Monday when his vehicle was found.
"Inside were found three telephones, a camera and a jacket," Ben Omar said.
He also said that Fowler's vehicle had been followed out of Niamey by an unidentified vehicle registered in Togo.
"These disappearances surprise us," Ben Omar said, affirming that security forces have been deployed in the area to try to find the diplomat.
Fowler, who was Canada's ambassador to the UN between 1995 and 2000, has twice travelled to Niger on business.
Niger's foreign ministry said in a statement it was "very concerned" about Fowler's disappearance, which it said occurred on Sunday "at about 6pm (17:00 GMT)".
"Since then and in spite of a search by defence and security forces in co-operation with the UN system, the ministry has been without news from Mr Fowler and his aides," the statement said.
In New York, Michele Montas, a UN spokeswoman, said that three people who were travelling in a vehicle of the United Nations Development Programme in southwestern Niger on Monday had been reported missing.
She did not give any details as to the identities of those people.