The European police agency Europol will now work with unnamed social media companies to track the accounts.
They aim to get new accounts closed down within two hours of them being set up.
Europol believes up to 5,000 EU citizens, including people from the UK, France, Belgium and the Netherlands, have travelled to territories controlled by IS.
Rob Wainwright, Europol's director, told the Guardian that the remit of the new team, which starts its work on 1 July, would be to "identify the ringleaders online".
But, he said, tracking all IS-linked social media accounts was too big a task.
Analysts at the Brookings Institution in Washington say the number of IS-linked Twitter accounts could even be as high as 90,000.
Recruited on social media
In February, three teenage girls - all pupils at the same London school - left their homes to go to Turkey, then Syria.
It later emerged that one of three girls, Shamima Begum, had been in contact on Twitter with the wife of an IS fighter.
A lawyer for her family said police were monitoring the messages and should have responded before she and her friends fled.
Aaron Zelin, an expert on jihadist groups, and a fellow of the Washington Institute, said that Twitter was generally used to draw in potential new recruits, not to directly hire them.
The more direct recruitment conversations take place on forums such as Skype, WhatsApp and Kik, he said.
Rita Katz, a director of the jihadi monitoring group Site, said IS militants regularly boasted online of ways in which to circumvent being blocked on social media.
In an article written in April, Ms Katz called for better security by social media firms and said simply blocking accounts was not enough.
She wrote: "It's time to stop shooting in the dark and recognize IS and its followers on Twitter are determined and dangerously adaptive - not because they enjoy tweeting, but because Twitter itself is among the most crucial tools to their growth and existence."
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