General Sir Nick Carter, the chief of the defence staff, said the British Army had done a “remarkable job” in Northern Ireland and false allegations against soldiers risked undermining the fighting spirit of the armed forces.
He said soldiers facing any investigation would be looked after “to the best of our ability”.
Sir Nick, speaking at a media briefing at RAF Coningsby in Lincolnshire, said: “It is right and proper that if our soldiers have done something wrong then they should clearly be investigated.
“But only if they have done something wrong.
“We need to have standards, we need to have values that people are held against otherwise we will lose the moral high-ground.
“What is fundamentally wrong, though, is if they’re chased by people who are making vexatious claims – and that will not happen on my watch. Absolutely not.
“If you end up with a clutch of vexatious claims then that undermines morale and has the risk of undermining our combat ethos and our fighting spirit.
“I would absolutely stamp on any of that sort of activity.”
Sir Nick’s comments come after his predecessor said he was “deeply uncomfortable” about veterans being investigated over their conduct during the Troubles.
Air Chief Marshal Sir Stuart Peach said deciding whether there should be a statute of limitations on inquiries into previous events was a political decision but he had concerns about investigating soldiers.
A consultation document issued by Northern Ireland Secretary Karen Bradley to deal with the legacy of the Troubles does not include provision for a statute of limitations.
Defence Secretary Gavin Williamson has said he will look at “all options” to protect veterans from legacy investigations.
Possible probes into conduct in previous conflicts has sparked fears that Second World War soldiers could also face being investigated.