Private schools that become integrated are able to retain their special character - usually a religious or philosophical belief - but receive a large boost in taxpayer funding.
The Ministry of Education's rejection of Destiny's proposal comes after the evangelical church was earlier turned down to run a charter school.
It is the third official put-down of the church, after an earlier application to integrate the school in 2009 failed.
Ms Williamson said the reason for the latest integration application was to give more South Aucklanders an opportunity to send their children to what was a very successful school. "We now need to reassess and look at some options and regroup and that's what we are currently doing."
Asked what those options were, and if they included a legal challenge, Ms Williamson declined to elaborate.
"We just want to see more children have the opportunity to participate in this education."
Katrina Casey, the ministry's head of sector enablement and support, said the application was declined late last year. She did not give the main reasons for the ministry's decision.
Integrated schools usually charge compulsory fees called attendance dues to meet property costs.
Destiny's application was opposed by the Post Primary Teachers' Association, which was concerned about how surrounding schools might be affected.
President Angela Roberts said smaller schools such as Destiny's, with a roll of nearly 190 last year, were relatively expensive to run, which would place more pressure on the overall public-school network.
About 12 per cent of the country's 2500 schools are state-integrated and about 4 per cent are private.
Staying private
• Destiny Church's application for its private school to become state-integrated has been declined.
• Integrated schools receive the same government funding for each student as state schools but retain ownership of school buildings and land.
