Upon his arrival at the premises of the famous temple, Mukherjee was accorded warm welcome by chief of Pashupati Area Development Trust Govinda Tandon and other members of the trust.
He was welcomed by 108 Batuk (Hindu boys) chanting 'Swasti mantras' amid musical resonance of panchai baja and thime baja (traditional musical instruments) after entering through the main eastern gate of the temple.
He performed a special puja called 'Rudrabhisekh', which includs bathing the Shiva Linga with 'panchamrit', consisting of milk, curd, honey, sugar and ghee, and lighting one lakh cotton lamps or 'lakh batti' at the holy Hindu shrine.
He spent more than 45 minutes while performing the puja, which is performed by donating a sum of 27,000 rupees to the treasury of the temple.
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While worshipping at the main temple, Mukherjee was assisted by a team of Indian priests, led by chief priest Ganesh Bhatta.
He also performed puja at Basuki Naag temple in the premises of the Pashupatinath by pouring milk, which is known as 'Dugdhabhisekh'.
Traditional drum and other instruments were played in Mukherjee's honour as soon as he arrived at the temple premises accompanied by Indian Ambassador Ranjit Rae amid tight security.
While keenly inspecting the shrine, the president also commented about the Bagmati river, according to chief of the trust Tandon.
The President said that Bagmati river was cleaner than what he saw seven years ago, when he visited there as the Indian External Affairs Minister, according to Tandon.
He also inquired about the damaged caused to the temple and its premises by last year's devastating earthquakes.
Very little damage was done to the Pashupatinath Temple by the earthquakes, Tandon said, adding that except a kitchen in the premises of the temple, no other structures were damaged.
In his remarks in the guest book of the temple, he wrote: "I am delighted to be here at the Pashupatinath temple once again. It is a place having cultural, religious and historical importance. I felt blissful after performing the special puja."
Tandon also presented a beautiful wooden idol to Mukherjee, who arrived in Nepal yesterday at the invitation of President Bidya Devi Bhandari as the first Indian president to visit the country in 18 years.