The order has seen MTN, Airtel and Glo all forced to block services with the government saying its move would last indefinitely due to Twitter's activities being “capable of undermining Nigeria’s corporate existence”.
The government further alleged that Twitter was facilitating "the spread of religious, racist, xenophobic and false messages" that "could tear some countries apart", a spokesperson told the BBC.
According to reports, Nigeria said it will prosecute anyone who breaches the ban.
Twitter said: "The announcement made by the Nigerian Government that they have suspended Twitter’s operations in Nigeria is deeply concerning. We’re investigating and will provide updates when we know more.”
The Nigeria Communications Commission (NCC) implemented the ban on Friday after Twitter deleted a tweet by President Muhammadu Buhari, that it said violated its "abusive behaviour" policy.
Last year Twitter suspended the NCC's account temporarily, however this was on security grounds. In a notice dated 24 November NCC said that suspension was a security precaution following a suspected hack attempt.
Meanwhile in India, Twitter has received a final warning from the government due to alleged non-compliance with new online safety rules.
In February, India announced new rules for social media firms that require the likes of Twitter, Google, YouTube and Facebook to appoint compliance officers. In a letter dated 5 June and seen by Reuters, the country's Ministry of Electronics and Information Technology said Twitter's chief compliance officer, and its grievance officer and nodal contact person were not employees as mandated by rules.
“The refusal to comply demonstrates Twitter’s lack of commitment and efforts towards providing a safe experience for the people of India on its platform,” the Ministry of Electronics and Information Technology said in notice on Saturday, adding it is giving “one last notice” to the site to comply as a “gesture of goodwill.”