Singh made the comments when Musharraf called him to offer his condolences for the death of 59 people, killed on Saturday when bombs exploded at two busy Delhi markets, a statement said.
"The Prime Minister told the President of Pakistan that the country was outraged at these heinous acts of terrorism," the foreign ministry statement said.
"Violence against defenceless civilians can never be justified, the Prime Minister said, and terrorism would never weaken India's resolve, or our commitment to the country's unity and territorial integrity," it said.
"The Prime Minister again drew the President's attention to Pakistan's commitment to ending cross-border terrorism and said we continue to be disturbed and dismayed at indications of the external linkages of terrorist groups with the October 29 bombing, and said India expects Pakistan to act against terrorism directed at India."
Although Singh referred to "external linkages" he did not name Pakistan, but Indian foreign ministry officials said he was referring to Pakistan.