During a joint press conference in New Delhi last week, Sarkozy urged Pakistan to combat extremists on its territory.
The foreign ministry in Islamabad said it had "conveyed Pakistan's disappointment" to the French ambassador over the remarks.
Pakistan also voiced its disappointment to the German charge d'affaires in Islamabad over Chancellor Angela Merkel's comments about Pakistan following her meeting with Singh in Berlin.
In view of Pakistan's excellent relations with France and Germany, the foreign ministry statement said, "Pakistan was surprised and disappointed at the reported remarks".
Recalling Pakistan's sacrifices in the fight against terrorism, it said, "incriminating Pakistan in the context of terrorism was unjustified and uncalled for".
Sarkozy said it was "unacceptable" that terror networks could find refuge in Pakistan and use it as a springboard to attack India, French troops in Afghanistan or other countries.
"It is unacceptable that India's security can be threatened by groups of terrorists acting from neighbouring countries," he said at Mumbai's Oberoi hotel, which was besieged by militants in November 2008.
The Mumbai attacks, which also targeted a Jewish centre, a popular tourist restaurant and the city's main railway station, killed 166 people, including two French nationals, and injured more than 300.
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