A safeguarding report found the search of the 15-year-old girl, known as Child Q, was unjustified and racism was "likely" to have been a factor.
In a statement the governing board said the school "was not aware that a strip-search was taking place".
Child Q is suing the Met Police and the school in Hackney over the incident.
The governing body said: "The incident involving Child Q is harrowing, and we understand and share the sadness and anger that is being felt by the community.
"While the school was not aware that a strip search was taking place, we wholly accept that the child should not have been left in the situation that she was.
"For this, we have offered a full and formal apology to Child Q and her family, and continue to work with them to provide what support we can."
Lawyers acting on behalf of Child Q have asked for the school not to be named in the media.
During the incident, the girl was taken out of an exam to the school's medical room and strip-searched by two female Met police officers who were looking for cannabis, while teachers remained outside.
No other adult was present, her parents were not contacted, and no drugs were found.
The girl's intimate body parts were exposed and she was made to take off her sanitary towel, according to the review.
Scotland Yard has admitted the actions of the two officers were "regrettable" and it "should never have happened".
On Monday, policing minister Kit Malthouse said the government was taking the matter "extremely seriously".
In the statement, the school's governing board said "changes were made immediately after the incident, and continued to be made".
Since the incident, the school has changed the leadership of its governing board. However, research by the BBC shows the chair of governors was still in place six months after the search occurred.
The make-up of the board has also changed. The governing board said it would not comment on the employment status of anyone involved.
The Independent Office of Police Conduct (IOPC) said a report on the incident is being "finalised".
The incident has sparked days of protest across Hackney, near the site of Child Q's school.