Fearful Israelis have been rushing to collect gas masks
"I don't see a direct link between Iraq and the hijackings and terror attacks in the United States," Major-General Amos Malka said in Israel's Yedioth Ahronoth newspaper on Sunday.
Some analysts have suggested that the scale of the attacks on the World Trade Center and Pentagon meant that a state must have been involved, with Iraq a likely suspect.
"I know many people are wondering whether this kind of attack could be carried out without the help of a country and they immediately point at Iraq or Iran," Mr Malka said.
US intelligence officials say they have found little evidence linking Iraq to the attacks.
Iraqi support
US President George W Bush has named Saudi-born dissident Osama bin Laden as the prime suspect in the attacks and has insisted that the US wants him "dead or alive."
On Thursday Jane's Security, a London-based publication specialising in defence and military information, reported that Israeli intelligence suspected Iraq of financing the attacks.
It identified Imad Mughniyeh, believed to be the head of overseas operations for the Lebanese group Hezbollah, and Egyptian Dr Ayman al-Zawahiri, a suspected member of Bin Laden's Al-Qaeda network as the organisers of the attacks.
And it alleged that they were financed and supported by Iraqi intelligence services.
Retaliation fears
Since the attacks Israelis have been bracing themselves for a US retaliation against Iraq.
There has been speculation that if Baghdad came under fire Iraqi President Saddam Hussein would respond by firing Scud missiles on Israel, as happened during the 1991 Gulf War.
The Israeli army has reported an increase in demand for gas masks at distribution centres throughout the country.
But in the interview Mr Malka said there was no reason for Israelis to panic.
He predicted that Iraq would only target Israel as a last resort.
"If Saddam Hussein does not feel personally threatened, he won't use the secret weapons he has been struggling to conceal," Mr Malka said.