Why is my cat peeing and pooping on my counter!?

I have a 4 year old cat. He is neutered and up to date on all vaccines. He recently had a vet visit and the vet said he is as healthy as a horse. He recently started pooping and peeing on my kitchen counters, and once on my living room floor. I have 3 litter boxes which I clean everyday. (I have another male cat that he has always gotten along with). He usually does it when he's gotten outside and we've brought him back in, or in the morning, if I take too long coming downstairs to feed him. The frequency has increased and I am at my wits end. Has anyone had this problem, and actually resolved it?