The price on a new education and training hub next to the Waterside Theatre has risen to an estimated £16.5 million.
The Waterside Academy was originally priced at £13 million but extra money is required to deal with a public space which is not part of the rental agreements of the academy, Waitrose or Travelodge.
Cabinet member for resources Neil Blake said: “The specifications have changed. It makes absolute sense to pay for it because someone has to do it.
“It will be an open usable space for everyone there.”
The four-storey academy will feature two restaurants and a cafe open to the public on the ground floor while the other floors will be taken over by Aylesbury College and Bucks New University.
Mr Blake said lessons had been learned since the overspend on the Waterside Theatre and that he is confident investment will bring a return for the council.
He added: “Everything has got to pay its way. While the theatre was criticised it has brought a significant amount of turnover to other businesses.
“It’s a hidden benefit and with 600 students coming into the town that’s 600 more who will be using the facilities.”
Mr Blake said the council was working to a maximum cost with the academy.
It is expected to built by the end of 2014.