A posse of policemen has been deployed outside the residence of Geelani and no one is allowed to enter or leave the premises, a spokesman of the Hurriyat said.
The police action came even as Jammu and Kashmir government said it will not allow "anti-India" activities in the state.
"No such rally or seminar will be allowed in the land of Jammu and Kashmir since we feel it will be anti-national activity," Deputy Chief Minister Nirmal Singh said. "The law will take its own course," he said, adding," no anti-national activity can be allowed on any part of the country."
Police officials refused to confirm or deny the house arrest of the separatist leaders.
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Geelani, while condemning the move, said the government has shown intolerance even to peaceful programmes.
"The government has completely buried the 'Battle of Ideas' slogan of the (Chief Minister) Mufti Mohammad Sayeed," Geelani said in a statement here.
The Hurriyat has planned to hold a seminar to which several separatist leaders, including from Sikhs groups, and Christian community representatives have been invited.
Those invited for the seminar include Akali Dal leader Simranjit Singh Mann, Dal Khalsa leader Kanwarpal Singh, noted human rights activist Gautam Navlakha and representatives of the Christian community.