Portkey Office

"Level Six, Department of Magical Transportation, incorporating the Floo Network Authority, Broom Regulatory Control, Portkey Office and Apparition Test Centre."

- Voice of lift at the Ministry of Magic

The Portkey Office was a division of the Department of Magical Transportation in charge of managing the usage and maintenance of Portkeys. Consequently, it seems like a reasonable deduction that the Portkey Office was responsible for authorising the creation of Portkeys (and possibly regulated their use once they had been created, as well).

Since Portkeys, according to Arthur Weasley, were often made from items that looked like rubbish, and since there were restrictions on enchanting Muggle objects for fear of their falling back into Muggle hands at some future date, it seems reasonable that objects enchanted to function as Portkeys would be kept track of.