There are renewed calls for a public inquiry after claims that haemophiliacs were not adequately informed of the risks of contaminated blood products.
Patients were infected through contaminated blood
BBC Scotland Frontline found evidence suggesting it took several years for some patients infected with Hepatitis C and HIV to be told of their condition.
It also questions the standards of facilities used to process blood.
The Scottish Executive said treatment was provided in good faith by health professionals involved at the time.
Hundreds of haemophiliacs were infected with potentially deadly viruses through blood products manufactured by the NHS.
About 550 patients received contaminated blood in Scotland in the 1970s and 1980s.
The Frontline investigative team has seen documents suggesting blood was processed in substandard facilities, from high-risk donors.
The Scottish National Blood Transfusion Service said the use of plasma from prison inmates was eventually phased out and admits that processing facilities were initially under pressure.
The service's medical director, Professor Ian Franklin, said: "We had the inspections and some of the reports were quite a challenge.
"But we had the inspections, we acted on them over time, and by the time we were required to have a licence, all of our facilities were licensed."
Some haemophiliacs said they were also badly let down, not just by the system but by their own doctors.
One who tested positive for HIV said he was not told for six years, whilst his doctor used his details for medical studies published all over the world.
Solicitor advocate Frank Maguire, who represents more than 100 Hepatitis C patients, said: "We must have an inquiry because the issues in Hepatitis C for which I want an inquiry have far-reaching repercussions.
"There are a whole lot of people out there who have been very injured, who have not had an explanation as to why they've been injured and we're not learning the lessons from it.
"There is also the risk of people being further infected."
Lawyers for patients have lodged papers at the Court of Session calling for a judicial review.
Mr Maguire said the review would apply to cases where people have died but, he added, "that doesn't necessarily help those who are still alive".
Only through a full public inquiry would all the issues be explored, he said.
Some patients claim doctors kept them uninformed
Raymond Bradley, a lawyer in the field of blood products and blood safety, said: "By 1982 it should have been appreciated that there was a significant risk of a serious illness, that is now identified as Aids, that was also blood-borne.
"Tragically, in many countries, there was a failure to act in respect of that particular risk."
BBC Scotland has also seen documents where haemophilia doctors and the blood transfusion service discussed the risks of HIV infection, but decided not to put a warning on Factor VIII blood products.
They said it would cause patients "unnecessary stress".
An executive spokeswoman said: "We have great sympathy with those affected and their families."
She added: "The treatment given to haemophiliacs was provided in good faith by the health professionals involved at the time.
"The risks of that treatment were not known at the time."
On Tuesday, the executive was defeated in a committee vote at Holyrood over the issue of payments to Hepatitis C sufferers.
Under the Skipton Fund the relatives of patients who died before 29 August, 2003, are not eligible for payments.
But MSPs on the health committee voted by five votes to two to remove the cut-off date.
There will now have to be a vote in the full parliament on the issue.
Scottish National Party health spokeswoman Shona Robison reiterated her support for an inquiry.
She said: "The people involved deserve nothing less than to have a public inquiry that can really try to get the answers to the many burning questions that they have."
Frontline Scotland's Blood and Tears programme will be broadcast on BBC One at 1900 BST on Wednesday.