A pig's head was left in the forward's locker by a team-mate on Thursday and, believing that Whelan was to blame, the Trinidad & Tobago international damaged his car.
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"I've apologised to Glenn Whelan for the destruction of his property, for all the people that think I did Michael Owen's car, I didn't. I just posted pictures of it, I was never involved in any of the pranks in the dressing room," he wrote.
"As far as tension in the squad, there's none, myself and Whelan had our thrash out and he said it wasn't him so I apologised and I'm paying for it."
Jones went on to admit that the perpetrator had yet to own up to the crime as he also demanded that those deeming the pig's head as "banter" should be prepared to accept the reaction.
"As for the person who did it, no one has come forward and apologised to me so I guess the joke was good then," he continued, "but, as I said, if you have the belly to take banter to that level, be willing to accept the reaction."