In a statement obtained by Aljazeera.net on Thursday, al-Qaida blamed US "crusaders" for the attacks.
"We say to all Muslims: we had nothing to do with this act," said the statement.
It charged the attacks were "an American plot aimed at provoking sectarian conflict between Muslims in Iraq".
"Our aims are clear: we are striking the American crusaders and their allies. We are striking the Iraqi police who are being used by the US to strike the mujahidin in Iraq."
"We are striking the agents of the US in the Council of Infidels, the so-called Governing Council and people associated with it, whether they are Sunni or Shia," the statement read.
But Iraq's top US official has blamed al-Qaida network for Tuesday's coordinated bombings in Karbala and Baghdad.
US occupation administrator Paul Bremer blamed Jordanian Abu Mussab al-Zarqawi for the attacks.
US officials blame al-Zarqawi for
the twin Iraqi bombings
Bremer said that al-Zarqawi, suspected of links to al-Qaida network, aimed to provoke sectarian violence between Shia and Sunni Muslim communities.
"Zarqawi and like-minded terrorists are in a losing race against time," he said on a day when thousands of Iraqi and Iranian Shiites took part in solemn processions as they buried their dead.
No evidence yet
Another senior US official said al-Qaida and Zarqawi were probably to blame, acknowledging however, that no evidence has been found connecting the group to the bombings.
"They (Al-Qaida) are a strong suspect, probably the prime suspect in facilitating these operations," he told reporters.
"Absolutely, it was Al-Qaida and the old regime," Muhammad Bahr al-Ulum, a Shia member of the US-appointed interim Governing Council, told AFP after visiting a hospital in the holy city of Karbala, south of Baghdad.
Some 200 people were killed and more than 500 wounded in Tuesday's bombings in the Shia holy city of Karbala and at a Baghdad mosque, the worst attacks in Iraq since the fall of former leader Saddam Hussein last April.
Iraqi authorities said 16 people were arrested over the attacks in Karbala, including 11 Iraqis and five Iranians, and said the bombers were financed from abroad.
"They were done by outside organisations," Police Colonel Karim Sultan said.
The judge investigating the attacks, Ahmad al-Hillali, also singled out al-Qaida and noted that the blasts happened almost at the same time as an attack in Pakistan's southwest city of Quetta that killed some 50 people.
"I believe the plan was for even greater carnage, and I think that joint action between Americans and Iraqis prevented that from happening."
US General John Abizaid
Polish arrest claims
In other developments, Polish officials said they captured two al-Qaida members days before the Tuesday attacks.
A spokesman for the Polish military on Thursday said they captured seven suspected al-Qaida members, two of them in the past week, prior to the Ashura attacks.
The senior US official added that foreign fighters may have crossed over the border with thousands of Iranian pilgrims who had come to Iraq to mourn a revered martyr freely for the first time in decades.
Blaming weak border patrols, Bremer added on Wednesday that the US would increase security along Iraq's borders.
"The US has committed 60 million dollars to support border security. We are adding hundreds of vehicles and doubling border police staffing in selected areas."
But securing Iraq's borders is no simple task as the country is nestled between six different countries: Kuwait, Saudi Arabia, Jordan, Syria, Iran and Turkey.
'Could have been worse'
As Shia leaders lashed out at the US-led occupying forces for failing them, the top US commander in Iraq told a US committee in Washington that things could have been even worse.
Iraq's vast borders stretch along
six different countries
Testifying before the House Armed Services Committee, General John Abizaid said US and Iraqi forces foiled a third planned attack in the southern port city of Basra and thwarted plans to attack several prominent Shiite personalities.
"I believe the plan was for even greater carnage, and I think that joint action between Americans and Iraqis prevented that from happening," he said.
As three days of official mourning for the dead were due to end Friday, Iraq's leaders were preparing to sign into law a new temporary constitution, pushed back two days out of respect for the victims.
Drawn up under the watchful eye of US officials after days and nights of political wrangling between leaders from Iraq's diverse religious and ethnic groups, the basic law is a big step on the road to winning back sovereignty.
The law will make Iraq a decentralised state with two official languages where Islam will be a source of legislation, but not the basis for it, making the text one of the most progressive in the wider Middle East.
The senior occupation official said the bombings had galvanised Iraq's interim leaders, who are focused on the 30 June date for a handover of sovereignty.
"The attacks in Baghdad and Karbala did not cause them to question their decision but to confirm their decision," he said.