Authorities took action after a citizen informed police on its emergency number that a black flag used by the dreaded militant outfit was waving on a pedestrian bridge on the Islamabad Express road.
Police later removed the trademark flag with inscribed message - 'Khilafat is coming'.
Interior minister Ahsan Iqbal took notice and asked Islamabad's Inspector General of Police to probe the matter and file a report.
Pakistan has repeatedly denied any organised presence of Islamic State (ISIS) in the country, but acknowledge that there might be some sympathisers in the country.
Army has already launched Operation Raddul Fassad to eliminate the supporters of the militants.
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