The accounts and their tweets were added to a public database that Twitter launched past year to track its battle against government-linked misinformation.
The removed accounts and their posts are being included in the company's public archive that tracks its efforts against government-linked misinformation. It is also adding a smaller number of deleted accounts linked to Russia, Venezuela and the Catalonia region of Spain.
Tech firms have been accused of allowing political propagandists to use social media to hijack elections, poison online debate, and smear their opponents. The remaining 2,865 accounts "employed a range of false personas to target conversations about political and social issues in Iran and globally".
But Twitter, in a blog post by its head of site integrity Yoel Roth, said "transparency is core to our mission" and vowed to fight "misleading, deceptive, and spammy behaviour".
Twitter first released the archive of data associated with known state-backed information operations last October to provide more transparency of information and to stem manipulation on its platform. A total of 248 accounts were engaged specifically in discussion about Israel.
The social-media company said most of the accounts were found to be spreading news stories angled to support Iranian geopolitical interests or to be fake user profiles created to manipulate online debate.
The St. Petersburg-based "troll factory" has been accused of working with Russian intelligence to influence Western votes, notably US President Donald Trump's election campaign.
"These removals are the result of increased information sharing between industry peers and law enforcement", Twitter said, regarding the fake Russian accounts.
And, in Spain, Twitter has taken down 130 allegedly fake accounts apparently set up to push the views of Catalan separatists.
Mr Roth said Twitter had collected all the suspect accounts it had removed since beginning its purge into a data set that it provided to researchers.