Shops, schools and business establishments remained closed due to the strike called by hard line Hurriyat Conference leader Syed Ali Shah Geelani and supported by several other separatist groups.
Although public transport remained off the roads in most parts of the valley, many private vehicles could be seen plying on the roads, official sources said.
They said stringent security measures were put in place for Mukherjee's maiden visit to the state since his election as the President.
Meanwhile, independent MLA from Langate Sheikh Abdul Rashid staged a sit-in alongwith nearly 100 supporters at Regal Chowk to draw Mukherjee's attention to Guru's mercy petition.
Rashid said he had voted for Mukherjee during the presidential election as he had promised to look into the Parliament attack convict's appeal for mercy.
There was no report of any untoward incident from anywhere in the Valley so far, official sources said.
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