The research says men are increasingly left on the sidelines of their families after break-ups and reveals cases where fathers have been blocked from seeing children who are in the care of substance-abusing former partners or living in chaotic households.
It calls for social workers to be retrained so that fathers are viewed with the same importance as mothers after family splits. One of the co-authors claims fathers receive a "raw deal".
Support group Circle Scotland says in the report, Listening to Fathers, that they need their own advocates to stand up for their rights. More support workers are also required in child care cases, it adds.
The charity provides holistic, community-based support to thousands of marginalised children and families in Edinburgh, West Lothian and North and South Lanarkshire.
Circle Scotland catalogued incidences of fathers being refused access to their children, despite them being left in the care of substance-abusing former partners who struggled to maintain a stable home environment.
Mark Smith, co-author of the report and senior lecturer in social work at the University of Edinburgh, said: "In social work, we need to recognise the complexity of a relationship and realise that problems are seldom caused by a 'bad man' at the end of it.
"We don't treat couples even- handedly. I think that men can get a raw deal."
Mr Smith warned that social workers are sometimes failing to recognise the changes in the post-industrial era, with many men taking a more practical role in fatherhood.
He added: "Men are allowed now to take on the more emotional and hands-on aspects of fatherhood which was maybe denied them when their primary role was as a breadwinner.
"In the past 10 years there has been a massive increase in the realisation of how important it is for fathers to be involved in their children's lives.
"At the same time, there has been an identification of men as being problematic within families, causing domestic abuse or child abuse, and within a profession such as social work, men can be perceived as scary at times."
He said some fathers react aggressively because of "frustration" over the way the system is treating them.
Co-author Nick Smithers, who works for the charity, added: "I thought I would be working with dangerous, risky men but in fact it was vulnerable men or men who found themselves in really difficult situations. I found myself advocating for the men or mediating with the authorities on their behalf."
Mr Smithers said most of his clients feel that their view is being ignored by the professionals, a situation which is compounded when they are aware the welfare of their children is at risk.
He added: "Of all the men I work with, I have not met anyone who does not care about their children, But they feel powerless and quite desperate."
Ian Maxwell, national development manager of Fathers for Families Scotland, said fathers no longer at home are often challenged about why they should be involved with their children. This is exacerbated if they are not married or do not have parental rights, he said, adding: "Many [fathers] have lived with their children and cared for them for many years but they are now being treated as a potential risk or as someone who isn't capable of looking after a child for long periods or overnight.
"Some social workers and other professionals seem to treat such fathers as of secondary importance. In doing so, they are ignoring all the evidence that fathers are just as important to children after separation as they were before."
Peter MacLeod, president of the Association of Directors of Social Work, said social workers had to adhere to strict codes of conduct and there was a formal complaints process.
He said: "In child protection cases, social workers are there to make sure that the best possible outcome is achieved for the child at the centre of the case."
Mr MacLeod added: "We would not accept that professionals systematically do not engage with fathers. It will sometimes be difficult to engage with fathers where allegations have been made against them and they are reluctant to discuss these matters."