Pakistan's foreign ministry said George Bush, who visited the region this month, should have offered similar deals to Islamabad and New Delhi to help their respective nuclear programmes.
In a statement on Friday, the ministry said the American plan will "only encourage India to continue its weapons programme without any constraint or inhibition".
On Wednesday, a bill was introduced to the US congress on Bush's behalf that would exempt nuclear-armed India from American laws that restrict the trade of nuclear material and equipment to countries that have not submitted to full nuclear inspections.
"The grant of [such a] waiver as a special case will have serious implications for the security environment in South Asia as well as for international non-proliferation efforts," the statement said.
Pakistan is an ally of the US in its war on terror, but Washington is refusing to share civilian nuclear technology with it, fearing that it could be transferred to other countries.
Pakistan became a nuclear power in 1998 when it conducted underground tests in response to India's nuclear tests, but some countries were alarmed in 2004 when a Pakistani scientist, Abdul Qader Khan, admitted passing information to Iran, North Korea and Libya.
Khan was initially detained but later pardoned because of his role in making Pakistan a nuclear power.
Pakistan and India are seeking more energy sources - including nuclear and natural gas - to provide for their huge populations and spur economic development.
Both countries are in discussions with Iran to build a pipeline to supply natural gas, but the United States opposes the proposal.
Officials from Pakistan, India and Iran met this week in Tehran to discuss technical, commercial and legal aspects of the pipeline, including pricing, the foreign ministry said in a statement on Saturday.
The statement said: "This was the first trilateral meeting at which substantial progress has been achieved."
Iran and India have been in talks
about a proposed gas pipeline
The next minister-level meeting will be held in Islamabad next month to discuss "outstanding issues".
Iran proposed the 2775km pipeline in 1996, but the project never got off the ground, mainly because of Indian concerns over its security in Pakistan.
The pipeline, expected to become operational in 2010, would supply around 60 million cubic metres of gas a day to India and up to 30 million cubic metres a day to Pakistan.