Ofsted inspectors visited St Peter's Collegiate School in Compton following a turbulent period which saw the former headteacher and chaplain leave in mysterious circumstances.
The education watchdog flagged up what it called "serious concerns" about safeguarding procedures which could have put pupils "at risk".
The suspension and subsequent departure of former headteacher David Lewis and an overhaul of governors has led to questions being asked about the running of the school by senior figures in the city over the last year.
St Peter's is overseen by the Diocese of Lichfield and is therefore outside of council control. The Diocese has not explained the reason for Mr Lewis' suspension.
Ofsted said the scale of leadership change in such a short space of time had "contributed to a lack of proper oversight".
Its report did not provide great detail about safeguarding concerns, but said child-protection policies had not always been followed. Inspectors also said foreign trips had taken place without proper risk assessments.
Its report said: "There have, in recent months, been several serious lapses in the application of safeguarding procedures that could potentially have put pupils at risk.
"These lapses have coincided with a period of considerable turbulence in senior leadership and governance in the school.
"Although safeguarding and child-protection policies have been, and continue to be, comprehensive and appropriate, they have not always been followed correctly by a small number of staff. For example, foreign visits have taken place without appropriate risk assessments having been completed. Concerns about the conduct of members of staff have not always been dealt with and reported to appropriate agencies in a timely manner."
Ofsted said the new leaders had vowed to address the issues but as they are so new to their posts it could not yet have confidence they would be able to do this.
A source close to the school suggested Mr Lewis was made a scapegoat for its troubles.
The source said: "Perhaps the Diocese of Lichfield should focus on their own failings rather than trying to blame anyone else."
Mr Lewis left in December 2019 having been suspended and away from the school for the best part of a year. No reference was made to his suspension when his departure was announced.
Former school chaplain Reverend David Weller also had his contract terminated in February 2019 following a complaint. The Diocese said the departures of the two men were not connected.
It prompted parents to raise concerns about "secrecy" surrounding changes in leadership.
A Diocese spokesman said: “The inspection acknowledges the period of significant change that St Peter’s has experienced as we have worked with the school to improve leadership and governance. While stating that the school’s safeguarding policies are fit for purpose and that vulnerable pupils are supported, the inspection also highlights occasions where unacceptable lapses have occurred and improvements are still needed.
“The inspection says that the leadership and management structures required to take the school forward and deal with these issues are now in place, including a new governing body and a recently appointed interim headteacher, supported by an executive leadership team.
“We will continue to work with the school to ensure improvement continues with the wellbeing and education of pupils remaining our priority at all times.”
Wolverhampton Council said it was supporting the school.
A spokesman said: "Although St Peter's Collegiate School is not a local authority-maintained school, safeguarding children and young people is a top priority for Wolverhampton Council.
"We are working with St Peter's to provide support at this time, and will continue to do so in order to address the issues highlighted by Ofsted."