The titles of 139 key files about HIV and infected blood transfusions that were missed by a supposedly thorough Department of Health internal search have been revealed through a freedom of information request.

The extraordinary oversights highlight, at the very least, the chaotic state of the department’s filing systems and will reinforce campaigners’ claims that there has been a cover-up to withhold embarrassing documents.

The full list of papers includes, for example, those labelled “Costing the care of HIV infections in haemophiliacs”, “Screening blood for high-risk donations” and “Blood screening for Aids”.

The potentially revelatory material has now been handed over to the infected blood inquiry, which began its hearings in London last week into a scandal that is estimated to have claimed more than 3,000 lives. Before effective screening was introduced, NHS patients were given transfusions and blood products in the 1970s and 1980s containing HIV and hepatitis C viruses.

As preparation for the inquiry, the Department of Health and Social Care (DHSC) carried out what was meant to be a comprehensive trawl through its records for anything that might be relevant. That exploration was then double-checked by the Government Internal Audit Agency (GIAA), which discovered a further “139 files likely to be directly relevant to the inquiry”.

In its report, the GIAA said: “It is our understanding that the [DHSC’s research management] team’s methodology should have identified these files … Therefore it is likely that the additional files identified in the searches we conducted were not filed with the correct prefixes, or were not initially identified due to pre-existing inconsistencies in the filing system.”

Jasons Evans, the founder of the campaign group Factor 8, submitted a freedom of information request asking for details about what the missed files covered. The titles released show that rather than relating to marginal issues, they cover the central questions being addressed by the inquiry.

The previously ignored files date back the 1970s and were evidently not available to earlier investigations such as the Penrose inquiry. Some are from as recently as 2009. A number are “defence litigation documents”, others transfusion service records.

One, from 1988, is entitled “Submission to the law officers on the lawfulness of certain types of anonymous testing for Human Immunodeficiency Virus (HIV)”. A few are records of the Advisory Committee on Dangerous Pathogens.

The files also include documents from the 1980s on the link between Aids and blood factor products, as well as investigations into the transmission of hepatitis C through transfusions. A series of files are labelled “Port screening – review of imported infection”.

Evans said: “Are we really supposed to believe the Department of Health accidentally missed 139 clearly relevant files? It really is one thing after another with them as they desperately cling on to their denial of liability for the contaminated blood scandal.

“The important thing here is that a number of these files that they apparently missed relate directly to litigation matters and legal advice. These are the files where we are likely to get a serious insight into the government’s legal thinking on these issues and so they are absolutely crucial.”

The infected blood inquiry, which resumes its hearings on Tuesday, is now assessing the significance of the files. Health experts and former ministers are not due to be called to answer questions until next year at the earliest.

A DHSC spokesperson said: “We are committed to being open and transparent with the inquiry and have waived the usual legal privileges to assist the process. We have already sent thousands of documents to the inquiry, and will continue to send more when necessary. The inquiry has always been free to request any files they wish to review and we will ensure these are shared as soon as possible.”