The tape appeared as US occupation forces killed 11 Iraqis who they said tried to ambush a patrol near the town of Balad, northwest of Baghdad.
In the taped message dated 14 June, Saddam said he was still in Iraq and warned Americans of more bloodshed.
US authorities said they would examine the recording, but said it was too soon to tell if the voice on the tape was that of Saddam.
But former Iraqi military intelligence chief, Wafiq al-Samarrai, told Aljazeera the voice and the expressions used were those of the deposed Iraqi leader.
He said this confirmed his theory that Saddam was alive and living in Iraq, moving around an area between Baghdad and Samarra, around 125 km north of the capital.
Saddam has not been seen in public since US-led forces ousted his government in early April.
Still in Iraq
"I am in Iraq and with a comrade...I tell you that I miss you, miss you, oh beloved people, even though I am among you and in your ranks," said the voice, adding that the recording had been made on 14 June.
The tape appeared on US Independence Day and a day after the occupation authority in Iraq offered a reward of $25 million for information leading to Saddam's capture or fate.
It also offered a $15 million bounty for information on either of Saddam's sons, Uday and Qusay.
Faced with daily attacks on US troops that it says are directed by former members of Saddam's Ba'ath party, the US has admitted failing to account for the ousted leader is hindering reconstruction efforts.
The voice on the tape urged Iraqis not to aid US and British forces in their attempts to hunt down the resistance.
"I call upon you to protect these heroic fighters and not give the invaders any information about them or their whereabouts during their operations," the voice said.
"There is resistance and I know you are hearing about this. Not a day passes without them (suffering) losses in our great land thanks to our great mujahidiin. The coming days will, God willing, be days of hardship and trouble for the infidel invaders," the voice added.
It said "jihad cells made up of Iraqi male and female fighters have been formed on a large scale" throughout Iraq to fight US-led forces occupying the country.
The voice also explained why the government fell so fast when US troops encircled Baghdad by saying "the previous government preferred to give up power than to become a puppet state".
Aljazeera's chief editor Ibrahim Hilal said the tape was delivered to Aljazeera via telephone on Friday.
"Someone called us and played back the tape for us and we recorded it. It ran for over 20 minutes, but only ten minutes are newsworthy. We don't know the source, or where the call came from. We have no reason to doubt its authenticity," he said.
The tape was the first purported to be from Saddam since the one received on 5 May by a reporter for the Sydney Morning Herald, who received a 14-minute audiotape from two men in Baghdad.
US troops' reaction
US occupation troops in Iraq vowed on Saturday to continue the search for Saddam Hussein loyalists. Sergeant Amy Abbott said the airing of the tape would have no bearing on the search for followers of the erstwhile Baath government.
The search for Iraqi fighters would continue north of Baghdad where the resistance against the occupation forces had been intense, Abbott said, adding it was an ongoing operation.