"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.
Search under way
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.
Niger is one of the world's poorest countries. The government is battling a Tuareg rebellion in the north, but the region where Fowler disappeared is well away from the area of conflict.