The Indian security agencies had raised concerns with Twitter that his account was being used to incite violence.
The Twitter had earlier also suspended Saeed's account @HSaeedOfficial. He then created a new ID on Twitter in December 2015.
Saeed is wanted by India for his role in 2008 Mumbai attack which killed over 160 people.
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In its bid to curb the spread of terrorism-related tweets on its platform, Twitter till early this year had suspended over 125,000 accounts for threatening or promoting terrorist acts, primarily related to the Islamic State (IS).
"Like most people around the world, we are horrified by the atrocities perpetrated by extremist groups. We condemn the use of Twitter to promote terrorism and the Twitter Rules make it clear that this type of behaviour, or any violent threat, is not permitted on our service," Twitter said in a blog post.