The Cabinet Office has warned it may not be possible to identify whoever used government computers to post "sickening" comments about the Hillsborough disaster.
The department said the passage of time and number of people using the Whitehall intranet made finding those who edited Wikipedia pages "challenging".
Relatives' groups and Liverpool-born MP Andy Burnham, a long-term campaigner on the issue, are being drafted in to monitor the investigation, a spokeswoman said.
The Liverpool Echo reported that revisions to the online encyclopaedia began five years ago on the 20th anniversary of the tragedy, and again in 2012.
Among the amendments to the Hillsborough section was an insertion saying "Blame Liverpool fans", and two years go the phrase "You'll never walk alone" was altered to "You'll never walk again" and later "You'll never w*** alone."
The Cabinet Office spokeswoman said: "The amendments made to Wikipedia are sickening. The behaviour is in complete contravention of the Civil Service Code. It is entirely unacceptable.
"This investigation is being led by the Cabinet Office permanent secretary, Richard Heaton, who is responsible for the Government computer network. He will be working closely with the director general for propriety and ethics and her team, as well as other senior officials.
"We are treating this matter with the utmost seriousness. Our first priority is to establish the facts and to examine the issues raised. Once we have the facts, we will update Parliament with the findings and consider further appropriate action. We will be keeping important stakeholders including the Hillsborough Family Support Group, the Hillsborough Justice Campaign, the Rt Rev James Jones, and the All Party Parliamentary Group on the Hillsborough Disaster updated.
"In addition we will invite the Rt Hon Andy Burnham MP, who has a deserved status as an expert on the disaster, to view all relevant material from the very outset and at every stage so that he can assure himself that all steps have been taken.
"At this time, we have no reason to suspect that the Hillsborough edits involve any particular department, nor more than one or two individuals in 2009 and 2012. As the first incident happened five years ago and there are hundreds of thousands of people on the Government's network, it may prove challenging to identify who was involved. But we are exhausting every option. Anyone with information should contact the Cabinet Office.
"No one should be in any doubt of the Government's position regarding the Hillsborough disaster and its support for the families of the 96 victims and all those affected by the tragedy."
Margaret Aspinall, from the Hillsborough Family Support Group, told the Echo the revelations had been deeply upsetting.
She said: "I don't even know how to react, it's just so sad. I hear something like that and it upsets me a great deal, it makes me incredibly sad. I'm glad somebody has found out about it but I'm frightened to be honest that we haven't known until now."
The Echo claimed the entries were made from IP addresses used by computers in government departments, including the Department for Culture, Media and Sport, the Treasury and the Office of the Solicitor General.
Further changes included altering the description of a statue of Liverpool's renowned former manager Bill Shankly on the Anfield Wikipedia page from "He made the people happy" to "He made a wonderful lemon drizzle cake".
A government computer was also reportedly used to change the phrase "This is Anfield", which is in the players' tunnel at the club's stadium, to "This is a S***hole".
A description of the Hillsborough memorial at Anfield was also changed to include "nothing for the victims of the Heysel stadium disaster", referring to the match in Brussels, Belgium, in 1985 between Liverpool and Juventus at which 39 people died.
Sheila Coleman, from the Hillsborough Justice Campaign, said it was "very saddening" that the changes came from within government and called for an investigation.
She told the Echo: "We're still in the inquests and we've sat listening to the most heartbreaking accounts of that day, and then you hear about things like this. It's absolutely appalling, disgraceful."
New inquests are being held into the deaths of 96 Liverpool fans who were crushed to death during the April 1989 FA Cup semi-final at Hillsborough in Sheffield.
They were ordered after new evidence revealed by the Independent Panel Report led to the quashing of the original 1991 inquest verdicts in the High Court in 2012.
Jon Davies, chief executive of Wikimedia UK, said the company was "appalled by such vandalism".
He said: "But our community have systems in place to deal with such incidents. In this case none of the offensive comments were up for more than a couple of hours, and most were removed within minutes."
According to Barry Collins, a freelance technology journalist, an identifier such as the computer's MAC (Media Access Control) address would be required to find out exactly which PC the Wikipedia edits came from. A MAC address is a unique code found in computer or networking equipment.
The former editor of PC Pro said: "The edit will show the IP address. That address will likely cover hundreds or thousands of PCs - it's highly unlikely to identify a single computer."