Scottish ministers were told in 2003 that the UK Health Department was investigating a claim that contaminated blood was being "knowingly supplied".
Newly released files show then health minister Malcolm Chisholm informed the Scottish Executive of the allegation.
Papers reveal recommendations for compensations levels were also discussed.
Thousands of people were given blood products infected with hepatitis and HIV in the 1970s and 1980s.
New testing procedures were introduced in 1991, but the allegation referred to by Mr Chisholm was made after the system was overhauled.
In September the first UK-wide inquiry into the public health disaster heard that more than 25,000 people could have been affected.
The scandal emerged after the UK government imported blood clotting factor from the US, where much of the plasma used came from donors, such as prison inmates, who sold their infected blood.
It was then given to haemophiliacs and other patients in the UK.
The 2003 documents also record Mr Chisholm telling the Cabinet he only had money for the cheapest of the options drawn up to compensate those given contaminated blood in Scotland.
The papers state: "Mr Chisholm said that there were two current issues in relation to Hepatitis-C infection through contaminated blood products.
"The first was the calls from Lord Ross, as chair of the Expert Group, in relation to the level of compensation for those affected and the range of people who should receive it.
"The second was a claim that the government had knowingly supplied contaminated blood after procedures had been introduced in 1991 to test for the virus used in blood transfusions.
"This would be a very serious matter, if true, and the Health Department was investigating the basis of the claim."
Earlier that year, in a briefing paper to the Scottish Cabinet, Mr Chisholm said he could only release up to £10m from the health budget towards a compensation scheme for those in Scotland given contaminated blood.
An expert group headed by Lord Ross recommended to a parliamentary committee that all those infected were given compensation payments, including to dependants of those who had become infected and died.
But Mr Chisholm said the scheme should be targeted at those still alive with long-term symptoms and signs of liver inflammation.
Scotland was the first part of the UK to hold an inquiry into the infected blood scandal, but this did not take place until 2009 and did not report until 2015.
The Penrose Inquiry, which was branded a whitewash by campaigners, said few matters could have been done differently and made only a single recommendation.
That was that anyone in Scotland who had a blood transfusion before 1991 should be tested for Hepatitis C if they have not already done so.
It estimated 3,000 patients in Scotland were infected with tainted blood products.
Last year the Scottish government announced increased compensation payments for those who contracted chronic hepatitis through contaminated blood, including to the partners of those who died.