Education bosses have this week revealed a second investigation has been launched into practices at troubled Long Lee Primary School.
But they are categorically refusing to explain the details surrounding the probe.
Bradford Council has opened a new inquiry following the outcome of a top-level probe into Sats results.
Local authority education boss Councillor Ralph Berry confirmed the initial investigation had uncovered “other areas of concern”.
He admitted the headteacher is currently not working at the school while his team looked into these “subsidiary issues”. But neither Coun Berry nor council officers would explain the nature of the investigation or the future of the head’s job, despite repeated requests from the Keighley News.
Both the school and governors refused to comment, and ward councillors were unable to shed light on the issue despite their own enquiries.
Coun Berry, the council’s executive member for children's services, said: “As a result of this investigation, a number of changes have taken place. The existing head is not at work at this time.
“All matters are being investigated thoroughly by the local authority in conjunction with the governors.”
The current crisis has grown out of an investigation last summer by the government’s Department for Education into alleged ;maladministration; of Sats tests at Long Lee Primary.
When the national performance tables were published in December, most of the school’s results were excluded while the investigation continued.
The 2013 results were last week visible on the national Sats website, and the government’s Standards and Testing Agency said it had completed its investigation.
A spokesman said: “Following this investigation, the decision was made to amend one child’s results for the English grammar, punctuation and spelling test.”
Coun Berry insisted that although other matters had come to light, the Sats were the main issue.
He added: “The most important point is we’ve moved to provide high-quality support leadership to the school for the education of the children.
“This is a school that has been doing well in recent years, and we have made a response to ensure this continues.”
Long Lee Primary is being run temporarily by the head of nearby Parkwood Primary School, Julie Butler.
A Bradford Council spokesman said Long Lee Primary has been receiving support from the council, including regular meetings with the chairman of governors and senior school leaders.
She added: “The governing body continues to work constructively with council officers and continues to focus on securing the best outcomes for children.”
The three Bradford councillors covering Keighley East ward, which includes Long Lee Primary, said they were unable to comment on the issue at the present time.