Theresa May personally blocked ministers from proposing a new legislation that could have protected veterans from prosecution for alleged offences during the Northern Ireland Troubles.
In an official memo, sent on behalf of the Prime Minister, it sets out instructions that unsolved murders during the Troubles "should not contain" proposals for a statute of limitations on historic prosecutions of veterans.
The leaked document, which was seen by The Sunday Telegraph, also said veterans should be offered "equal, rather than preferential, treatment" to other groups covered by the consultation, which included terrorists.
"The Prime Minister has decided that the consultation document should not contain specific reference to a 'statute of limitations' or 'amnesties', in line with government policy.
"The Ministry of Defence should work closely with the Northern Ireland office to ensure that their veterans package offers equal, rather than preferential, treatment relative to other groups or individuals affected by this consultation."
The document, dated March 2018, was said to have been written by Mrs May's assistant private secretary.
Tory MP Johnny Mercer, who has campaigned to protect veterans from repeated investigations into historical allegations, described the memo as a "sucker punch", saying he found the comments "genuinely appalling".
"That troops, uniformed and sent by the Crown to an unpopular, difficult and bloody war, should not have the Government, at least starting, on their side is totally unacceptable," he told The Telegraph.
There are currently six veterans who are facing prosecution for their involvement in the Northern Ireland Troubles.
Demonstrations have been taking place across the UK against the prosecutions.
The Defence Secretary Penny Mordaunt says the issue of historical allegations is a priority for her.
Last week Ms Mordaunt announced plans for legislation to provide stronger protection from repeated investigations into historical allegations for veterans of overseas conflicts in Iraq and Afghanistan.
Under the proposals, there would be a "presumption against prosecution" in relation to alleged incidents dating back more than 10 years, unless there were "exceptional circumstances".
However, currently, the legislation will not apply to those who served in Northern Ireland.
A Government spokesman said: "The Ministry of Defence have proposed legislation to provide better support and stronger legal protections for serving and former personnel facing investigation over alleged historical offences overseas.
"This will ensure veterans are not subject to repeated investigations many years after the events in question where there is no new evidence.
"A separate consultation has been run by Northern Ireland Office on how to deal with the past in Northern Ireland, and the conclusion of that will be announced as soon as possible."