In 2012, the annual day student fees were $9775, in 2013 they have risen by $1152 to $10,927 annually.
The annual fee for a full boarder will rise by $2094 to $21,869.
When the Chronicle called Mrs Jex-Blake, she said she couldn't comment because she wasn't the board chairman any longer.
"You need to contact the new chairman, Brodie Stevens,"she said.
Mr Stevens could not be contacted.
In the letter, Mrs Jex-Blake says a detailed breakdown of the 2013 fee structure would be given after January 27.
Collegiate School registrar Alan Richardson said yesterday nothing would be said publicly about the fees until January 27, when state integration starts at Collegiate.
"Then there will be a nationwide statement from Education Minister Hekia Parata about the integration, the fees, the new commissioner, everything that will be happening throughout the integration process. I am sorry I am unable to say anything anything, but we have been specifically told not to by the ministry."
The December letter also says the Whanganui College Board of Trustees would remain responsible for the seven-day boarding school model and preserving the special character within the integrated school structure.
The board intends to appoint a commercial director and boarding/special character director, who will report to it.
The Minister of Education has appointed a governance facilitator, Andy van Ameyde, to guide the school into state integration, which starts on January 27. Integration of the school was announced on November 2.
Mr van Ameyde is the co-ordinator of the Christian Schools Network and chairman of the board of trustees of Middleton Grange School in Christchurch.