An investigation by this newspaper has found there are no burial records for children who lost their lives while in the care of the Sisters of Nazareth, which operated four homes in Scotland and at least 17 south of the Border.
In addition, only two Scottish councils were able to confirm the whereabouts of children who died while in residential care and were buried in common ground.
The De La Salle Brothers, a Catholic order of monks which also operated a number of children's homes in Scotland, is also thought to have retained no burial records.
Only Quarriers appears to have bucked the trend, as the Scottish charity has a database of all 345 children and young people buried at Mount Zion Cemetery in Quarrier's Village, Renfrewshire. The church and its grounds have now been turned into luxury flats, although there is a memorial in the cemetery.
The concerns over burial records add to the growing pressure on Scottish ministers to sanction a public inquiry into abuse in Scottish children's homes.
Independent expert Tom Shaw was appointed to look into the issue by the Labour/Lib Dem administration in 2004 after a number of scandals came to light.
Among his findings, which were published shortly after the SNP came to power three years later, was the fact that senior officials had ordered "records to be destroyed".
His report stated: "Visits to graveyards showed that children who died in children's residential establishments are buried there although it is unknown how many due to poor record practices. Some children lie in unmarked graves."
It added: "No central government databases exist of children's residential establishments in Scotland between 1950-1995."
Since then, Holyrood has spent millions of pounds on a number of measures, including confidential talking shops and academic studies - which many victims find unhelpful and intrusive.
However, several other countries - including Canada, Australia, New Zealand, the Republic of Ireland and now Northern Ireland - have opted to hold public inquiries to help expose the perpetrators and their crimes.
The issue of unmarked graves has been highlighted by Frank Docherty, who discovered that at least 150 children from Smyllum Children's Home in Lanark had been buried in unmarked graves in the town.
After a high-profile campaign, the Daughters of Charity of St Vincent de Paul - another order of nuns with close links to the Sisters of Nazareth - finally installed a memorial to them at St Mary's graveyard in 2003.
In recent years, another memorial has been appeared to say that youngsters from another nearby institution - the St Charles' Certified Institution for "mentally defective Catholic children" at Carstairs - were secretly buried there as well.
Mr Docherty, himself a former Smyllum resident, has spent more than a decade attempting to discover where the children who died in Britain's Nazareth Houses are buried, but to no avail.
He said: "We have got some records but they are very sketchy. [The Sisters of Nazareth] say that only 19 children died in the whole of the 1900s but a lot more than that died.
"Smyllum was open for 117 years and there are at least 150 children buried in the graveyard. Children in these homes died all the time, sometimes from pneumonia and sometimes from different diseases."
Mr Docherty added that some former residents of a Nazareth House in the north of England have claimed that stillborn babies were simply buried "beneath the flowerbeds".
A spokeswoman for the Sisters of Nazareth General Archive, at Nazareth House in Hammersmith, London, told the Sunday Express: "Unfortunately we do not hold any burial records for children in the archive, so I am unable to answer your questions."
Sources within the Catholic Church insist that in most cases "they were contractors to local government" and it should have been up to councils to keep burial records.
However, following a Freedom of Information request, only two councils were able to pinpoint the graves of children who died in orphanages and were buried in common ground.
East Dunbartonshire Council has records of unmarked graves for youngsters from both Waverley Park Home in Kirkintilloch and Lennox Castle Hospital in Lennoxtown.
Highland Council, meanwhile, said that 10 burials took place in Tomnahurich cemetery in Inverness of children who lived at The Highland Orphanage.
In Northern Ireland, the Historical Institutional Abuse Inquiry is investigating 13 institutions and both the De La Salle Brothers and the Sisters of Nazareth have apologised to victims of abuse.
However, no such apology has been offered in the rest of the United Kingdom. There is a further complication for campaigners in Britain, where a House of Lords ruling means that no civil claims can be brought after more than three years.
This has resulted in around 600 claims for compensation from Scottish childhood abuse victims being abandoned.
Helen Holland, who suffered at a Nazareth House in Kilmarnock in the 1970s, agreed that almost every children's home would once have had an area of unmarked ground for burials.
She said: "It would certainly make you think along those lines. I'm certain there were deaths when I was in Nazareth House. I remember one child jumping off the fire exit and there was no way she could have survived. We were all sent to bed early that night and not told anything about what had happened, but we never ever saw that child again."
There is a modern marble headstone to around half a dozen former Nazareth House residents at Kilmarnock Cemetery, however it is not known when this was installed.
Ms Holland added: "I did a bit of investigation work myself and even went down to Kilmarnock to check the records. In the early 1980s some of the ground at Nazareth House had been sold off and the building work had to stop because they unearthed skeletal remains of children.
"I remember reading it in the Kilmarnock Standard when my sister sent it down to me while I was living in London. A few years ago I went into the offices to check the archives but all the copies from that era had been destroyed by a burst pipe.
"I remember it clearly though, and I remember the sisters saying the bodies must have belonged to plague victims."