Theresa May has told defence chiefs "every effort must be made" to stop the legal system being abused and British troops hounded.
The Prime Minister hailed Britain's armed forces as the "best in the world" and stressed her determination to prevent vexatious claims being brought against them.
It comes amid mounting criticism of the Iraq Historic Allegations Team (Ihat), which was set up to investigate allegations of murder, abuse and torture by British troops.
Former soldiers have claimed they have been hounded through the courts on unfounded claims and there are growing calls for Ihat to be shut down.
Mrs May raised the issue during an in-depth meeting with defence chiefs during which she also discussed the fight against Islamic State (IS), also known as Daesh.
She met Chief of the Defence Staff Air Chief Marshal Sir Stuart Peach, the heads of the Navy, Army and Air Force, and senior civil servants during the 90-minute update.
A spokeswoman for the Prime Minister said she told of her pride in the British armed forces and stressed that abuse of the legal system must be prevented and troops protected from vexatious claims.
She also discussed tackling the migrant crisis in the Mediterranean and air strikes against IS in Iraq and Syria.
Mrs May said: "The men and women of our armed forces do an incredible job, often making huge sacrifices to keep us safe.
"Whether taking the fight to Daesh in Iraq and Syria, helping to tackle the migrant crisis in the Mediterranean or providing flood relief at home - we owe them a huge debt of gratitude.
"Our armed forces are the best in the world and with the biggest defence budget in Europe and the second biggest in Nato we will continue to play our part on the world stage, protecting UK interests across the globe."
MP Johnny Mercer, a member of the Defence Select Committee who is heading an investigation into Ihat, has branded the legal pursuit of troops "a national disgrace" and called for the team to be axed.
Mrs May was also briefed on the Royal Navy's efforts to protect shipping against pirates off the Horn of Africa and on measures being taken to develop a more diverse workforce across the defence branches.