A trouble-hit St Helens secondary is investigating an incident involved two Liverpool FC youth players at the school.
Bosses at Rainhill High confirmed to the Reporter the incident was between two students but declined to reveal the nature of the complaint.
However, they did state it was NOT related to allegations of sexual harassment again female teachers at the schools.
Rainhill High provides education to Liverpool FC academy players from outside the Merseyside region.
Past pupils include Manchester City winger Raheem Sterling.
A school spokesman said: “Rainhill High School is investigating an incident between two students, this is not safeguarding related.
“It is important to respect the privacy of the children concerned.
“We can confirm that the Daily Telegraph story about Rainhill High School currently investigating allegations of sexual harassment against female teachers is not true.
“All of the children at Rainhill deserve to continue to receive their education without media intrusion.”
Rainhill High has been at the centre of a number of controversies over the past 18 months, including bully allegations by striking teachers.
Liverpool FC also confirmed it was aware of the investigation.
A spokesman for Liverpool FC said: “We are aware Rainhill High School is currently looking into complaints made against two of their pupils who are also young players at Liverpool.
“The club will allow the school to conclude its own inquiries in the first instance before considering their findings.
“Until the school completes its own process, the club will not be making any further comment.”