Making it clear that Washington wants Islamabad to continue taking tough measures to revive its economy, Clinton said "we have made it clear...that we think it is a mistake to reverse the progress that was being made to provide a stronger economic base for Pakistan".
Her strong comments came as IMF in a sharp rebuke to Islamabad asked it to cut its energy subsidies saying they were crippling its economy.
Labelling fuel subsidies as "inefficient and untargeted", IMF spokesman Caroline Atkinson said energy subsidies were going to high income people and large companies and were consuming large part of the budget.
The sharp reactions from the US Secretary of State and world's top financial institution, which is bankrolling Pakistan with huge loans came as the country's beleaguered Prime Minister Yousuf Raza Gilani bowed to political pressure and reversed the controversial fuel price hike.
The move was apparently aimed at saving his fragile government from collapsing as major Opposition party PML(N) served an ultimatum to the PPP-led government to roll back the fuel hike or they would back a no-confidence motion against the government in parliament.
"We have made it known to Pakistan government on many occasions that it must reform its economic laws and regulations, including those that affect fuel and its cost," Clinton told reporters at a joint appearance with her Japanese counterpart.
US officials said Pakistan government can ill afford to increase its public expenditure after last year's catastrophic floods which have raised fears that the country cannot meet IMF targets on inflation and budget deficit levels.
Mark Toner, a state department spokesman had earlier signalled US Opposition to the reversal of fuel price hikes saying that Washington had been impressing on Islamabad to keep steady on the reform process as these were important for the country's long term economic stability.
"Our position is that Pakistan needs to undertake difficult economic reforms that are going to require some pain, frankly politically," he said in reply to questions about Pakistan's fuel price rollback.
Islamabad's decision to rollback fuel hike could endanger its ability to receive funds under the IMF's USD 11 billion loan programme, sources said.