Bob Ainsworth said his thoughts were with the dead soldier's family and friends
The defence secretary has said the Afghanistan mission is vital to the UK's national security, following the 100th military death of this year.
Bob Ainsworth joined calls for the public not to judge the campaign by casualties alone as he arrived to visit troops in Helmand.
Head of the Army Gen Sir David Richards said such a judgement "undervalues the tremendous efforts" of the UK troops.
It comes as the body of the 99th UK serviceman to be killed was flown back.
Meanwhile, hundreds of people gathered in Wimborne, Dorset, for the funeral of 20-year-old Rifleman Philip Allen - of 2nd Battalion The Rifles - who was killed in an explosion in Afghanistan on the eve of Remembrance Day.
We are told we mustn't think too much about casualties - we must think about the propaganda, the lies, the posturing that we have been subjected to for the last eight years
The British soldier, of 1st Battalion The Royal Anglian Regiment, was shot in the Nad-e Ali area of Helmand on Monday afternoon. He has not yet been named but next of kin have been informed.
Gen Richards said the latest "loss hardens our determination to succeed".
He added: "The temptation to judge this essential campaign by casualties alone undervalues the tremendous efforts of our forces and our allies, and the progress they are making."
The chief of the defence staff, Air Chief Marshal Sir Jock Stirrup, admitted 2009 had been a "particularly challenging year" but said the sacrifices "have brought security" to more of Helmand.
He warned there was "still much to do, and there will be difficult days ahead".
But Sir Jock said: "Our armed forces are making a real difference, and are building the basis for enduring success in Afghanistan."
AFGHAN WAR DEATH TOLLS 2009
Afghan forces: More than 680 believed killed or missing
Source: iCasualties.org; various
Former Chief of the General Staff, Gen Sir Richard Dannatt, told BBC Radio 4's Today programme that Prime Minister Gordon Brown was now, "late in the day... beginning to get" the significance and importance of winning in Afghanistan.
Mr Brown announced last month that 500 more UK troops would be going to Afghanistan, taking the total UK deployment to more than 10,000, while the US plans to boost its deployment by 30,000.
But BBC security correspondent Gordon Corera says there is a recognition that increases in British and American troop numbers are unlikely to reduce the casualty rate in the short term.
The total number of UK troops killed since the start of operations in Afghanistan in October 2001 has now reached 237.
One Labour backbencher has accused ministers and military leaders of producing "carefully manicured soundbites" in response to the 100th death.
Newport West MP Paul Flynn said they were seeking to suppress debate on whether forces should be in the country by presenting a "fiction" of potential success.
In a Commons debate he said: "We are told we mustn't think too much about casualties, that we must think about other things - we must think about the propaganda, the lies, the posturing that we have been subjected to for the last eight years."
The Stop the War coalition said it would be intensifying its campaign to have troops withdrawn.
The body of A/Sgt John Amer was driven through Wootton Bassett
The group will deliver a petition to Downing Street on 21 December.
In a speech in London, shadow defence secretary Liam Fox said the UK was carrying a "disproportionate" burden in Afghanistan.
He said Nato countries which failed to contribute troops or financial support to the military mission in Afghanistan should ask themselves whether they were serious about their membership of the alliance.
Earlier, Afghan President Hamid Karzai warned that it would take 15 years before Afghanistan was able to pay for the costs of maintaining its own security forces.
KEY COALITION GAINS IN HELMAND
Lashkar Gah: Capital of Helmand, home to main British command and Provincial Reconstruction Team (PRT) made up of British civilian and military personnel. International organisations and PRT have funded new schools, roads and parks. Population: 200,000.
Garmsir: Secured by US Marines and British troops after heavy fighting in 2008. Prince Harry served here. Cited as a success story by Ministry of Defence, with flourishing bazaar, school, own police force and Afghan army working with US marines to keep Taliban at bay. Population: 100,000.
Sangin: Centre for opium trade and historically sympathetic to Taliban. Taken by Nato-led International Security Assistance Force troops in 2007. MoD says town is safer now thanks to British and Afghan military presence and new checkpoints. Population: 30,000.
Musa Qala: Occupied by British forces since bloody battle in December 2007. Still attracts Taliban attacks. Population: 20,000.
Gereshk: Major British base, regarded by the MoD as "one of the most stable areas in Helmand" - but 30 British soldiers killed in the area in the past three years.
Babaji and Nad Ali: Although no longer controlled by Taliban, coalition forces still fighting to keep area secure.
Kajaki: Scene of heavy fighting from February 2007 to September 2008, when British secured strategic dam, now being rebuilt.
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