"Hurriyat is not against the yatra... We have always treated the pilgrims in a humane and friendly manner with traditional hospitality and this will continue in future as well," he said in a statement before he was detained by police.
Geelani was detained when he tried to leave his Hyderpora residence to offer Friday prayers at a local mosque in the outskirts of the city.
Hurriyat has certain "genuine concerns" with regard to the policies of the shrine board and wants to see the yatra to be carried out in a disciplined manner.
"Attempts are being made to give communal hue to our genuine concerns by showing that we are against the yatra, which is not true," he said and alleged that a conspiracy has been hatched to trigger communal violence in Jammu on the issue in an attempt to separate the region from Kashmir.