"We do not believe that a reference to the World Bank is justified," foreign ministry spokesman Navtej Sarna told reporters.
"Our view has been that during detailed discussion there had been some convergence.
"And we believe through further talks, further convergence can be promoted," Sarna said.
The decision, casting a shadow over the nuclear rivals' sluggish peace process, follows the breakdown of months of talks between Islamabad and New Delhi over the Baghliar Dam in the part of the divided Himalayan territory under Indian control.
It is the first time Pakistan has sought outside involvement in a World Bank-brokered water-sharing treaty which it signed with India in 1960. The agreement has survived two wars between the South Asian foes.
The water treaty bars India from interfering with the flow of the three rivers feeding Pakistan -- the Indus, the Chenab and the Jhelum -- but allows it to generate electricity from them.
Pakistan claims the dam could block water from the Chenab river and cut vital irrigation in Pakistan's wheat-growing Punjab province. India says the fears are groundless.
"It was determined that Pakistan was left with no choice but to go to the World Bank," an official statement said after a high-level meeting chaired by Prime Minister Shaukat Aziz.
Pakistan and India began a step-by-step peace process in January 2004 to solve key issues, including the core problem of Kashmir, which is split between India and Pakistan but claimed in full by both.