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Gen David Petraeus was addressing about 1,700 guests at the US embassy in Kabul after arriving to take over command.
He said that military-civilian cooperation was "not optional".
Gen Petraeus is replacing Gen Stanley McChrystal, who was sacked after he and his aides mocked and criticised top US officials in a magazine article.
US Defence Secretary Robert Gates has now ordered a tightening of the rules covering the US military's dealings with the media.
'One mission' Gen Petraeus was addressing Afghan, American and other international guests on the lawn of the embassy on Saturday.
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We'll keep at it. We'll persevere. We're committed for the long term
Karl Eikenberry US Ambassador to Afghanistan Pakistan post-McChrystal US tightens military media rules "This is an effort in which we must achieve unity of effort and common purpose. Civilian and military, Afghan and international, we are part of one team with one mission," Gen Petraeus said.
"On this important endeavour, cooperation is not optional," he said.
Gen Petraeus has already warned that the conflict may become more difficult before major improvements are won.
He and US President Barack Obama have both insisted a change of personnel at the top does not mean a change in strategy.
Gen Petraeus said on Saturday: "This is a tough mission, there is nothing easy about it. But working together we can achieve progress and we can achieve our mutual objective."
Media rules have tightened in the wake of McChrystal's sacking Gen Petraeus is to meet President Hamid Karzai later on Saturday.Gen Petraeus faces a number of tough challenges over the coming months, including reducing casualties. June saw the highest number of deaths among Nato personnel in the nine years of war - 102.
He will also have to oversee the escalation of operations against the Taliban in Kandahar province - a campaign that has been postponed until September.
He has promised to use the same counter-insurgency tactics he used in Iraq and that Gen McChrystal introduced in Afghanistan earlier this year.
Gen Petraeus has also pledged to look at the application of the current rules of engagement.
These are designed to reduce civilian casualties but some US troops believe they put them at too great a risk.
US Ambassador to Afghanistan Karl Eikenberry welcomed Gen Petraeus at the embassy gathering, saying: "Welcome aboard. You are welcome at this embassy 24-7."
Mr Eikenberry said of the Afghan strategy: "We'll keep at it. We'll persevere. We're committed for the long term."
Mr Eikenberry was one of the US officials criticised by Gen McChrystal in the Rolling Stone article that led to his sacking.
President Obama, Vice-President Joe Biden, National Security Adviser James Jones, US ambassador to Afghanistan Karl Eikenberry and the special US envoy to Afghanistan and Pakistan, Richard Holbrooke, were also targeted.
Mr Gates has now tightened the rules covering the US military's dealings with the media, saying he was "concerned that the [defence] department has grown lax in how we engage with the media".
The Pentagon insisted the new order was not linked to the McChrystal incident and was not meant to be a gag.
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