IT took more than a decade of campaigning to secure a public inquiry into how hundreds of Scots became infected with hepatitis C and HIV through contaminated NHS blood products.

But as the public hearings of the Penrose inquiry drew to a close on Friday – almost three years since it got under way – campaigners say the inquiry was so flawed that the truth of how the scandal unfolded may never be known.

Concerns have been raised that despite around 80 victims and their families volunteering to play a key role in the inquiry, only 15 were selected as "core participants" and just six were permitted to tell their stories in person. It is estimated that at least 1000 people died, and hundreds more were infected, due to contaminated blood products given during transfusions throughout the 1970s and 1980s.

The Sunday Herald also discovered that more than 240 Government files concerning blood policy were not available to the inquiry because they had been destroyed. According to evidence submitted by Scottish Government officials, nearly half of the 560 such files dating back to 1970 have been disposed of since 1998.

Victims insist their fight for justice will continue following the publication of the inquiry report by Lord Penrose, which is expected to be unveiled in early 2013.

Four years ago the Scottish Government announced the inquiry would be set up to examine how haemophiliacs and other patients were infected. Philip Dolan, convener of the Scottish Infected Blood Forum, who was infected with hepatitis C during treatment for haemophilia, is among those who fought for a judicial investigation. He fears the Penrose inquiry will be a "whitewash", due to issues such as the small number of patients who were allowed to give oral evidence.

He said: "Doctors came and gave evidence that they told patients such and such, but there was not the opportunity for patients to say what has been said was not true. We had hoped the outcome of this would be helpful, but at the closure it doesn't seem to be. One would like to be optimistic but the failure to let people be heard raises questions as to what we can expect."

Dolan also highlighted concerns about the destruction of files, claiming it was consistent with other documents "disappearing".

Written evidence submitted to the inquiry by Scottish Government officials states that 242 files were destroyed "in line with normal records management processes".

Just over two-thirds were disposed of before 2005, but files were destroyed as late as 2007, by which time the campaign for an official inquiry had been under way for a number of years.

On Friday, the last of the public hearings took place in Edinburgh, after 89 days involving 60 witnesses.

In closing submissions, legal representatives for the victims and their families highlighted issues such as an understatement of the risk posed to the blood supply from HIV "long after it must have been known that there was a significant danger", and an "unnecessary risk" taken by continuing to collect blood from prisons until early 1984.

Simon Di Rollo QC also criticised an attitude of "defensiveness" at the inquiry, despite no intention to "go after" individuals, saying: "Why is it so hard for institutions like the NHS, and government departments responsible for its administration, to admit publicly mistakes and misjudgments?

"If the submissions on behalf of the NHS and Scottish Government are to be taken at face value, then no mistakes were made, no regret is expressed and communication with patients was as good as it possibly could have been ... A fearless recognition, where appropriate, that mistakes were made, would be so much more constructive and beneficial for everyone."

However, Rory Anderson QC, representing the Scottish National Blood Transfusion Service and health boards, said it was disappointing that the deaths and infections were still described as a "scandal".

He said: "No doubt some will say - that certain things might have been done differently or that different decisions might have been taken. That may or may not be correct. But of this there should be no doubt: there is no justification for the description of events as 'a scandal'. There is and was no scandal, that word always carrying with it the connotation of wrongdoing of one sort or another."

Bill Wright, chairman of Haemophilia Scotland, said: "There will never be total closure on this issue for those that have lost loved ones."

Despite the loss of documents, a Scottish Government spokeswoman said there were "robust file management procedures in place", adding: "We are confident the number of papers not delivered have been kept to a minimum and are generally of low relevance to the inquiry's investigations."

A spokeswoman for the Penrose inquiry said individual "core participants" were selected by Lord Penrose to reflect the different interests and experiences of patients and relatives.

She added: "It was never expected or intended that all core participants would give oral evidence ... In addition to those who gave oral evidence over 150 patients and family members gave written statements."

She would not speculate on what might have been contained in the destroyed files and therefore the impact of their loss to the inquiry, adding: "The inquiry can only proceed on the evidence available."