Sayeed Ansari, a spokesman for the Afghan intelligence service, said the authorities had evidence of the direct involvement of the ISI, citing documents uncovered during the investigation into the attack, confessions from 16 suspects detained afterwards, as well as mobile phone contacts.
But he gave no further details and failed to name officials within the ISI who might have been involved.
With regard to Monday's blast, Humayun Hamid Zada, a spokesman for the Afghan president, said: "The sophistication of this attack and the kind of material that was used, the specific targeting ... everything has the hallmarks of a particular intelligence agency that has conducted similar terrorist acts inside Afghanistan in the past."
"So we have sufficient evidence to say that."
ISI in Afghanistan
Although it might seem a little early to point the finger at Islamabad for the embassy bombing, the charge highlights the history of the ISI in Afghanistan.
The Soviet-Afghan war of the 1980s saw the enhancement of covert operations by the ISI, under the auspices of General Zia ul-Haq, a former president, but primarily aided by the US Central Intelligence Agency (CIA).
A special Afghan Section was created to oversee the co-ordination of the war.
A number of officers from the ISI's Covert Action Division received training in the US and many intelligence experts from the CIA assisted ISI members and Afghan mujahidin in their operations against Soviet troops.
These fighters and supporters later formed the Taliban movement, and the subsequent government that was toppled in 2001.
However, defence analysts believe the ISI has stopped operating in Afghanistan.
Ikram Sehgal, a former major in the Pakistan military, told Al Jazeera that Pakistan's intelligence agency is no longer involved in Afghan affairs.
"This is a ridiculous claim by the Afghan government. The ISI would have to be stupid to attempt to further destabilise Afghanistan.
"The CIA was also involved in Afghanistan, do you think it is only Pakistani intelligence that was involved historically?"
Sehgal also said that Islambad is facing too many internal problems to focus its efforts across the border.
Asad Durrani, a former director-general of the ISI, agrees: "I can understand that Pakistan would be the first suspect as it was supposed to be behind the Taliban resistance, and now [with] the Indian embassy involved, you have a history between Indo-Pak relations."
"But ... because we have so many problems within our country and the problems along the tribal areas .... and now ... for us to open another front - the Indian front - that has been quiet for the past four to five years, does not make any sense to me ... unless someone here has gone off their rocker, has gone beserk."
While the ISI officially focuses on "counterterrorism operations" in a post-911 political climate, many still believe it is an invisible force in Pakistani politics and numerous incidents beyond the country's borders.
What is certain, however, is that the allegations made against the ISI are just that - allegations. No specific member of the ISI has been named, or bought to account.