A spokesman for Mourinho said: "The incident occurred because of a misunderstanding over documents required for veterinary regulations.
"Mr Mourinho would like to make it clear that his pet dog was bought in England from a reputable breeder and has had all its necessary inoculations.
"Full co-operation will be given over any animal health issues."
Mourinho, 44, was attending Chelsea's player-of-the-year awards where Michael Essien received the top gong when he was called to his home on Tuesday, according to reports.
The Portuguese manager of the Stamford Bridge club is believed to have refused to allow the police to take the Yorkshire terrier.
Scotland Yard confirmed the dog was to be seized under the Animal Health Act of 1981 and Rabies Order Act of 1974.
"A 44-year-old man was arrested on suspicion of obstructing police and was taken to a west London police station," said a police spokesperson.
"He subsequently received a caution for obstructing police."