The speaker, purportedly Abu Musab al-Zarqawi, spoke on an audiotape posted on the internet on Wednesday.
He also announced the formation of a new command to fight Iraq's biggest Shia militia.
His comments appeared aimed at discouraging armed Iraqi groups from entering talks with the Iraqi government and challenged critics who maintain that fighting US troops is legitimate but attacking Iraqi forces is not.
Defence Secretary Donald Rumsfeld and other officials have said US representatives have participated in meetings with Sunni fighter groups in an effort to help the Iraqi government draw them into the political process.
"Some say that the resistance is divided into two groups - an honourable resistance that fights the non-believer-occupier and a dishonourable resistance that fights Iraqis," the speaker said.
"We announce that the Iraqi army is an army of apostates and mercenaries that has allied itself with the Crusaders and came to destroy Islam and fight Muslims. We will fight it."
The speaker tacitly acknowledged pressure to abandon the struggle against the Americans and their Iraqi allies, saying he was "saddened and burdened" by people "advising me not to persist in fighting in Iraq".
"We announce that the Iraqi army is an army of apostates and mercenaries that has allied itself with the Crusaders and came to destroy Islam and fight Muslims. We will fight it"
Internet message attributed to Abu Musab al-Zarqawi
"How long will the people of knowledge stay away from the battlefield of jihad, issuing verdicts and giving advice that are far from the reality that the nation is living?" he asked.
Fight to the end
In an impassioned defence of the resistance, the speaker said al-Qaida was willing to fight to the end "so that the women are freed from the prisons of the Crusaders and the spiteful Shia".
"Some want us to end our jihad in Iraq," he said. "God has ordered us to fight the non-believers... We think that the nation is committing a sin by failing to support the mujahidin."
He said the Americans began speaking of negotiations to end the conflict after al-Qaida had "humiliated" US forces on the battlefield.
"Didn't they (the Americans) plan to turn against Syria and its people after invading Iraq under the pretext that it is giving refuge to Baathists and is not stopping the infiltration of fighters?" he said.
The speaker said a new unit would
'eradicate' the Shia Badr Brigade
"God thwarted their plans through the strikes of the honest mujahidin. They're still keen on carrying out their plan and moving in that direction to enable Israel to control the area from the Euphrates to the Nile," the tape said.
It was impossible to determine whether the speaker was al-Zarqawi, although the voice sounded like ones on tapes US officials have acknowledged were made by the Jordanian-born man accused of being the mastermind behind many of the bloodiest attacks in Iraq.
It could not be determined when the speech was delivered, although the speaker refers to codenames for US military operations launched in recent weeks.
The speaker said al-Qaida in Iraq would soon unveil a new unit, the Omar Corps, to "eradicate" the Badr Brigade, a militia of the country's biggest Shia party, the Supreme Council for the Islamic Revolution in Iraq.
Al-Zarqawi's attacks against Iraqi Shia, who make up an estimated 60% of the country's 26 million people, have raised fears that the country could descend into civil war.