He also criticised what he called Islamabad's reluctance to crack down on fighters operating in their territory.
Rejecting Singh's comments, the Pakistani foreign ministry said such accusations could undermine already tense relations between the two nuclear-armed rivals.
"[They] not only ratchet up tensions, but occlude facts and destroy all prospects of serious and objective investigations into the Mumbai attacks,'' the ministry said in a statement.
Earlier Shivshankar Menon, India's foreign secretary said he found it "hard to believe" that an attack of the scale of that in Mumbai "could occur without anybody, anywhere in the establishment knowing that this was happening."
|The attacks on multiple targets in Mumbai left 179 people dead [GALLO/GETTY]
His comments came after Indian officials handed Islamabad evidence they said clearly showed the Mumbai attacks originated in Pakistan.
The attacks on multiple targets in India's financial capital lasted for nearly three days and left 179 people dead with hundreds more wounded.
Singh's comments, his most forceful yet on the issue, stopped short of directly accusing Islamabad of aiding the attackers, but the Indian government has faced growing political pressure to take a tougher stand against Pakistan.
Although he did not directly name any Pakistani officials or agencies, New Delhi has previously accused the Inter-Services Intelligence, the country's military-controlled spy agency, of being involved in attacks against India.
On Tuesday Asif Ali Zardari, the Pakistani president, called for recognition of his country's efforts to crack down on fighters operating in Pakistan's remote and mountainous borderlands.
"We expect our friends to have the same understanding, to rise above these stateless actors who are trying to create a problem in the region,'' he told reporters in Afghanistan on Tuesday.