The results of a freedom of information request sent to all 32 local authorities in Scotland revealed patchy arrangements for supporting "looked after" 16 and 17-year-olds in having their say in September's poll.
The University of Strathclyde and Who Cares? Scotland, who jointly submitted the requests, say young people would normally be supported by their families to register to vote and to think about the issues. The report argues councils, as so-called corporate parents, should fulfil that role instead.
However, the survey found that whilst most councils have plans to encourage participation by young people in their care in the referendum, few have put them into action. The deadline for registration is September 2.
The report describes examples of the best support currently on offer to young people in general, or in relation to those in care in particular.
In analysing the survey results, Dr Graham Connelly, of Strathclyde's School of Social work and Social Policy, identified four categories: councils which planned direct action with young people in care, and had already started it; those with plans for direct action they hadn't put into practice yet; those which had unimplemented plans for indirect action, and those which had taken indirect action. Direct action included providing newsletters or personal letters to looked after young people, or speaking directly to 15 to 17-year-olds who will be eligible to vote.
Indirect action covered information aimed at foster carers, advice to carers on registering young voters, or generic reminders sent to key services working with young people in care.
All 32 local authorities had planned some action, but only six had already taken direct action and eight had taken indirect action, a total of only 42 per cent of councils.
Those planning to engage directly with young people in care amounted to 19, or 58 per cent, of councils.
Examples of good practice included one council which had registered all young people in its children's homes to vote.
Another - Aberdeenshire - had included an article about the referendum and how to register to vote in a newsletter on children's rights sent to all children looked after away from home. It said: "It is really important that you get whoever you are living with to help you register to vote. Speak to your foster carer, your kinship carer, your key worker or your social worker if you need further information or help."
However, other councils do not appear to plan to contact all looked after young people, or are using a definition which excludes young people who are looked after in their own home.
Dr Connelly said he was disappointed to find that direct action was in short supply. "It does worry me these young people who are marginalised anyway may be disenfranchised in the referendum.
"Voting for the first time is a considerable responsibility. Yet our research found that few local authorities are providing support directly to their looked after young people in relation to registering to vote.
"There are likely to be discussions going on in households with young people across the country about the referendum. Parents will often help young people when they get to vote and that starts with getting themselves registered. But who is doing that with looked after children?"
Local authorities have what are known as "corporate parenting" responsibilities to young people who are and have been in their care, he added. "It struck me as interesting and quite a practical test of that corporate parenting role."
Mr Connelly said the independence referendum held a particular interest for young people. "This is an opportunity for them to make a decision with consequences for their lives in the future. As many young people as possible need to take it."
Robbie Lyons, a 16-year-old care leaver said: "Being brought up in care we are literally children of Scotland. It's so important young people get registered and have their say."
He said those local authorities which have plans should put them into action and ensure young people are engaged. "It's not enough just to give someone a leaflet or a form and expect democracy to happen. As our corporate parents, local authorities must support us to get involved and to have a say," he added.
Who Cares? Scotland has created an online hub of information for young people and those involved in supporting them, including details of how to register. This can be found at www.whocaresscotland.org/care-to-vote.