The church has made two unsuccessful bids to convert its private Christian school, on the City of God premises on Druces Rd, Manukau, into a state-integrated institution.
Applications for two new charter schools close in October.
Williamson rejected concerns over Destiny's earlier application.
She said the school fitted the criteria, including being near over-crowded state schools and targeting Pacific Island and Maori students.
She said "non-Destiny" students attended the school.
Education Ministry deputy secretary Graham Stoop said applications closed on October 30 and contenders had to offer innovative approaches to teach struggling students in areas not well-served by a state school.
The first five charter schools were opened last year and four others opened earlier this year.
The Weekend Herald reported yesterday that some schools were paying hundreds of thousands in governance fees to owners.
Administration and management costs formed up to 40 per cent of some of the school's salary payments.
In contrast, state school principals said administration staff pay varied from 10-25 per cent.
Last week, the Government altered the funding model for new charter schools with set establishment payments up to $400,000, six months property and principal salary and funding linked to student numbers.