On Wednesday, police said they had produced the boy in court, asking for 25 days remand to complete investigations.
Raju Adhikari, the investigating officer, said the arrested boy had identified the other culprits but all of them had gone into hiding.
Ekka was badly shaken by the incident.
'I would not like to go back to Baniyatar,' he said. 'I tried to help somebody who needed help and this is how I was treated.'
The attack comes two months after an explosion in one of Kathmandu valley's biggest Catholic churches killed three women, two of whom were Indians.
Last year, another Indian priest, John Prakash Moyalan, was killed by armed bandits in his residence in southern Nepal.
Moyalan's murder and the church blast were planned by the same man, a 38-year-old Hindu extremist whose underground organisation, the Nepal Defence Army, is seeking to restore Hinduism as the state religion and revive monarchy.
'The India-Nepal hostility is affecting Catholic priests as well,' said Lawrence Maniyar, former principal of the St Xavier's School that is being targeted by unions led by the Maoists.
'At a meeting with the union representatives, they told us dismissively, you people from Kerala think you can run things in Nepal,' Maniyar said.
'We can't explain to them that we are not here because we are Indians. We are here because we are Catholic priests. We belong to an international organisation and take up our stations wherever we are asked to by our superiors.'