Demand for match tickets was high, and with priority given to season ticket and voucher holders only 1000 tickets were left when they went on general sale on Thursday - despite the club initially expecting between three and four hundred to be left at that stage.
Fans queued from as early as 6am, and with fans lined up round the entire ground the final ticket was sold at midday - with around a thousand fans turned away despite queueing for upto two hours.
"From my point of view it is a tragedy if any of our regular ardent supporters have missed out and I feel desperately, desperately sorry for them," said Wharton.
"If any really genuine regular fan has missed out I would like them to write to me and explain how it came about that they didn't get a ticket.
"I am desperately sorry for them but I want to learn from it if anyone has any information to make it better. We can hopefully make sure that the situation does not happen again."
Wharton has also re-iterated his intention to step down as chairman of the club at the end of the season if the club do not win promotion, a statement he also made last season before being convinced to stay on.
"A game like Leeds does not tempt to to stay on as chairman beyond the end of the season," he said.