Bola Ogun was speaking after it emerged that Damilola had told his father he was regularly bullied by other pupils at Oliver Goldsmith Primary School in Peckham, London.
His mother, Gloria Taylor, had also approached teachers about the problem before his death.
Mr Ogun, who said the school was now "trying to return to some semblance of normality", insisted action had been taken following Mrs Taylor's complaints.
"The school has a very robust attitude towards any form of bullying and any complaints which are brought before the school are taken extremely seriously," he told BBC News 24.
"That's why in situations such as that the head would be keen to meet the parents.
"What will then happen, and did happen in this case, is that where we can identify specific individuals that were involved in it the school will use its rigorous behaviour policy to take action."
Pressed further he said: "Absolutely, action was taken".
He said that following Damilola's murder, as he walked home from a school computer club, school officials met relatives to explain what had been done about his mother's complaints.
However, Mr Ogun said it would be "inappropriate" to give further details.
He did say the school had been "bearing up pretty well" in the aftermath of the killing.
"From the start of the week when everybody was in shock and in disbelief, towards the end of the week people are trying to return to some semblance of normality."
Attendance and schoolwork has continued as normal, thanks in part to the efforts of parents to support the school.
Attention is focused on looking after the children and a counselling plan for pupils who needed it has been set up, Mr Ogun explained.
Speaking hours after the arrest of three people in connection with the murder, Mr Ogun commended the police operation so far.
He added: "The sympathy of the school and the whole community are with the family."
"We are very much thinking of them at this time."
In the aftermath of Damilola's death, Oliver Goldsmith's head teacher, Mark Parsons, said he was proud of his school's anti-bullying policy and was satisfied the death was not connected with the school.
"I am totally convinced it is something outside the school," he said earlier this week.
"The allegations of bullying related to name calling and slight scuffles. It was not the type of bullying that would lead to this type of violence."
New guidance
Separately, it has been reported that schools are to be given new guidance on how to deal with bullies as part of an initiative planned before the death of Damilola.
According to The Times newspaper, there will be a move away from the existing "no blame" method of dealing with the problem, which relies on mediation and counselling, rather than punishment.
Parents will be invited to meet school inspectors in private if they are worried about bullying, and victims may be offered assertiveness training.