The directive comes a day after widespread violence and arson following the conviction of sect chief Gurmeet Ram Rahim Singh in a rape case led to at least 31 people being killed and 250 injured.
"We have ordered a search of all 'naam charcha ghars' (congregation centres) of the Dera Sacha Sauda wherever located in Haryana," state Additional Chief Secretary (Home) Ram Niwas told news agency PTI.
"We have asked security personnel to conduct searches at all Dera centres thoroughly and seize any weapons found," he added.
The search operation would include the Dera headquarters in Sirsa and the congregation centre in Panchkula, where a CBI court pronounced its judgement against the self-styled godman.
"All those who died in Panchkula were rioters. The intention of the rioters was to ransack Panchkula," Mr Niwas said.
He added that 28 vehicles, mostly belonging to the media, were torched by the rioters and 524 persons have been arrested. "We have asked the media whose vehicles have been set afire by rioters to get FIRs registered and provide video footage of the violence," he said.