The researchers uncovered the lurking networks while probing Twitter to see how people use it, the BBC reported.
Some of the accounts have been used to fake follower numbers, send spam and boost interest in trending topics.
The largest network ties together more than 350,000 accounts and further work suggests others may be even bigger.
As of the third quarter of 2016, the microblogging service averaged at 317 million monthly active users.
"It is difficult to assess exactly how many Twitter users are bots," said graduate student Juan Echeverria, a computer scientist at the University College London (UCL), who uncovered the massive networks.
Echeverria's research began by combing through a sample of 1 per cent of Twitter users in order to get a better understanding of how people use the social network.
However, analysis of the data revealed some strange results that, when probed further, seemed to reveal lots of linked accounts, suggesting one person or group is running the botnet.
The researchers are now asking the public via a website and a Twitter account to report bots they spot to help get a better idea of how prevalent they are. Many bots are obvious because they have been created recently, have few followers, have strange user names and little content in the messages.
The network of 350,000 bots stood out because all the accounts in it shared subtle characteristics that revealed they were linked. These included: tweets coming from places where nobody lives; messages being posted only from Windows phones; almost exclusively including quotes from Star Wars novels.
"Considering all the efforts already there in detecting bots, it is amazing that we can still find so many bots, much more than previous research," Zhou said.
A Twitter spokesman said the social network had clear policy on automation that was "strictly enforced, the report said.
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