Asadullah Khalid, who heads the National Directorate of Security, was injured in a grenade attack in a spy agency guesthouse, police said.
A former cabinet minister and a key anti-Taliban figure, he was nominated to head the NDS by President Hamid Karzai in August and approved by parliament despite objections from Western rights groups and accusations that he tortured detainees.
The intelligence agency confirmed the attack.
"The Afghan intelligence chief has survived a cowardly terrorist attack in the city of Kabul," the NDS said in a brief statement. "The case is under investigation."
There were few details on the nature of the attack. Witnesses heard an explosion. Police said Khalid was wounded by a grenade, but unconfirmed reports by senior government officials said it had been a suicide attack.
Neither was his condition immediately clear.
A security source told AFP that Khalid had been rushed to hospital and given major blood transfusions. A Western diplomat told AFP that Khalid was "seriously wounded".
There was no immediate word on what had happened to the attacker.
Neither was there any immediate claim of responsibility but Taliban insurgents waging a war to topple the government will be suspected of being behind the assassination attempt.
Khalid is fiercely anti-Taliban and close to the Karzai family.
His appointment was interpreted as part of an effort by the president to secure his power base before anointing a successor to stand for election in 2014.
The NDS plays a crucial role in the fight against the Taliban, who were ousted from power by a US-led invasion in 2001 for harbouring Al-Qaeda leader Osama bin Laden after the 9/11 attacks on New York and Washington.
Their influence on the conduct of the war is likely to grow as the US and NATO withdraw the vast bulk of their combat troops from the country by the end of 2014 and hand responsibility for the war to Afghan security forces.
Amnesty International had urged parliament to delay its approval of Khalid, asking lawmakers to investigate claims of his "involvement in numerous alleged acts of torture and other grave human rights violations".
The London-based rights group said he had been linked to numerous cases of torture and unlawful killings over the past decade, while serving as governor of Ghazni province from 2001-05 and of Kandahar from 2005-08.
It also said there were credible allegations that Khalid was involved in the bombing of a vehicle that killed five UN workers in Kandahar in April 2007.
Afghan police and other security forces are increasingly targets of Taliban attacks as they take a bigger role in the fight ahead of the NATO withdrawal.
Karzai cannot stand for re-election in 2014, having served the two terms permitted under the constitution, but is widely seen as seeking to hand over power to a family member or a hand-picked successor.
There are widespread fears that Afghanistan could once again plunge into chaos and a civil war after the NATO withdrawal, particularly if the 2014 elections are fraudulent.
"There is a real risk that the regime in Kabul could collapse upon NATO's withdrawal," Candace Rondeaux, analyst for the International Crisis Group, said in report in October.
"The Afghan army and police are overwhelmed and underprepared for the transition," said Rondeaux. "Another botched election and resultant unrest would push them to breaking point."
Earlier Thursday, officials said the Afghan government had decided to scrap a UN-backed election watchdog in favour of a tribunal that could give Karzai more control over the polls.
The controversial decision to scrap the Electoral Complaint Commission (ECC) was taken Monday, but requires approval from parliament to come into effect.
The ECC, made up of three Afghans and two foreign UN representatives, investigated complaints related to the 2009 elections.