They don't need permission from the owner of the motel to search.
Once a motel owner rents a room, it shifts to the guest to allow people into their room. It works the other way, too. Your farther cannot consent to a search of a guest's room after it's been rented - he has no legal authority to consent.
If the police have reasonable suspicion of criminal activity, they can detain and question people for a reasonable period of time to investigate. If those people consent to searches (or if there are other grounds to allow a search, such as the person is on probation or parole), then the police can legally search.
Something tells me that your father's motel has become a target of local police - the two things that come to mind are that prostitutes or drug dealers are frequent guests and they're conducting their illegal activity in the hotel.
Perhaps instead of complaining, he should ask to speak to a detective or a supervisor in the detective bureau in the police agency that's doing all the searches. He can try to find out what's going on and clean the place up, ending the frequent police visits.