Johnny Mercer, the veterans minister, said he was sorry to have been “relieved of my responsibilities”.
Earlier it was reported that he was on the brink of resignation over the government’s handling of historic prosecution of soldiers.
No 10 confirmed last night he had left government.
A Downing Street spokesperson said: “This evening the Prime Minister has accepted the resignation of Johnny Mercer as minister for defence people and veterans. He thanks Johnny Mercer for his service as a government minister since 2019.”
At the same time Mr Mercer tweeted: “I’m sorry to have been relieved of my responsibilities in Government tonight.”
In a letter to the prime minister, also posted on his Twitter account, Mr Mercer said: “It is with a heavy heart that I am forced to offer you my resignation from your government.”
He said that he had hoped Mr Johnson’s premiership would “signal a step change in veterans affairs in the UK”.
He added: “Whilst we continue to say all the right things, you will understand that if we fail to match that with what we deliver, we risk damaging an already bruised veterans cohort further, as I told you last month in our first face to face meeting, we crossed that line some time ago.”
Mr Mercer left government just hours after the government announced it was to exempt genocide and torture from controversial new legal safeguards for British troops serving overseas.
The Ministry of Defence (MoD) said that ministers will table their own amendment to the Overseas Operations Bill when it returns to the Commons tomorrow.
Last week the House of Lords voted by 333 to 228 to support a change to the Bill to ensure the most serious offences were not covered. The legislation is designed to protect service personnel from vexatious battlefield claims.
It was prompted in part by a number of prosecutions of soldiers who served in Northern Ireland during the Troubles.