Albanian counterterrorism police searched the Iranian embassy after staff were expelled over a counterattack it blames on Tehran.
Iranian diplomats burnt papers inside the premises after diplomatic ties were severed over the cyberattack.
It is the first time a country has cut diplomatic ties with another over a cyberattack.
Edi Rama, the Albanian prime minister, blamed the cyberattack, which took place in July, on the Islamic republic and gave its diplomats 24 hours to leave the country.
Officers armed with automatic rifles entered the building after two cars with diplomatic plates had left, Reuters reported.
It said a man had earlier been seen inside the embassy throwing papers into a rusty barrel.
In a video address to the nation, Mr Rama said the cyberattack has “threatened to paralyse public services, erase digital systems and hack into state records, steal government intranet electronic communication and stir chaos and insecurity in the country”.
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The US, Albania’s closest ally, also blamed Iran for the attack and promised to “take further action to hold Iran accountable for actions that threaten the security of a US ally”.
Tehran decried Tirana’s decision to cut ties over what it described as “baseless claims”.
The cyberattack temporarily shut down several Albanian government digital services and websites on 15 July.
Ties between the two countries have been fraught since 2014, when Albania sheltered around 3,000 members of the Iranian opposition group Mujahedeen-e-Khalq, or MEK, after they left Iraq.
Albania has previously expelled four Iranian diplomats in two separate instances in 2018 and 2020 for “threatening national security.”
