Mr Aitken is pressing Peter Peacock, Education Minister, to find ways of acknowledging the interests of this group, since 30 per cent of pupils are involved.
In a letter to Mr Peacock, Mr Aitken stated: "At a recent conference at which I was speaking on the support for fathers and the challenge for public services, I was approached by one non-resident parent with reference to the recent consultation on parents' involvement.
"This parent made the point that 30 per cent of all school pupils have a non-resident parent and yet the consultation made no reference to the particular challenges they have in being involved in their child's education."
He added: "The challenge schools have is not to become caught in the crossfire between parents whose break-up is full of animosity, but still to ensure that the children involved get the support they need from both their parents where that is possible.
"Of course, where there has been domestic violence, drug use or whatever, that is even more difficult, but certainly there needs to be a recognition of the significant numbers of pupils whose home life involves a non-resident parent, whatever the reason for that being the case and that did not happen in the context of the parental involvement consultation."
Mr Aitken, executive member for children and families on Edinburgh City Council, has asked his own authority to review its procedures to see if there was more it could do or a different approach it could take.
A spokeswoman for the Scottish Executive said: "We have no plans to issue specific guidance on this issue. We expect local authorities to take steps to ensure that all parents can be involved in their children's education.
The provisions of the Scottish Schools (Parental Involvement) Bill will apply equally to both parents - absent or otherwise."