The agencies acted after receiving reports that the water and power and environment ministries had absolved themselves of negligence in the matter, The Dawn newspaper quoted its sources as saying.
Arrests of some officials "could not be ruled out", the report said.
The records of the ministries were seized following "Indian aggression on (Pakistan's) water rights and securing international carbon credits on hydropower projects disputed by Pakistan", the report said.
Inter-ministerial correspondence over the lapse continued for over nine months and "crucial objections over adverse environmental impact of the projects nearing completion on the Indian side had not yet been officially taken up with New Delhi", the daily quoted its sources as saying.
The water and power ministry said it was not responsible for the lapse because it was the job of the Pakistan environmental protection agency to conduct an environmental impact assessment.
The ministry said it had no role in ratifying trans-border impact assessments, whose documents had not been shared with it.
The environment ministry washed its hands of the matter and said that since the Indian projects were of a strategic nature, it could not have intervened unless its attention had been drawn to the issue and professional advice sought, the report said.
The intelligence agencies took away the record of the 'Manual of responsibilities -- Indus Waters Treaty 1960' issued by the office of the Commissioner for the Permanent Indus Commission in 1971.
The 72-page manual defines responsibilities of the defence, interior, Kashmir affairs, industries and natural resources ministries, met department, provincial governments, railways and water and power development authority.
The prime minister's office had in July last year asked the of water and power, foreign affairs and environment ministries to explain how India had secured carbon credits from the United Nations for the Chutak and Nimmo-Bazgo hydropower projects that Pakistan claims have violated the Indus Waters Treaty.
These ministries were taken by surprise by India's success in getting carbon credits without clearance of cross-border environmental impact assessment reports of the projects by Pakistan.
This happened at a time when Islamabad's representative was heading a forum of the UN Framework Convention on Climate Change that approved such credits.
Water and Power Secretary Javed Iqbal ordered an inquiry to establish how officials of the ministry and Pakistan's permanent Indus waters commissioner had delayed pursuing technical objections over these two projects and a number of others being built by India.
These projects include the Kishanganga hydropower plan, which has now been taken up with the international court of arbitration.
Officials said the lapse might have already compromised Pakistan's opposition to the projects.
