He said when India pursued the matter, Pakistan had given the papers pertaining to the detention of Saeed in 2002 and 2009.
During his talks with Malik, Shinde said Pakistan has been told that it was of "paramount importance" to bring those guilty of the terror strikes to justice to ensure that the Indo-Pak peace process proceeds in an atmosphere free of terrorism and violence.
"On a larger plane, it was stated that terrorism is affecting all aspects of the relationship and that we must deal with this menace effectively," he said.
In the Lok Sabha, senior BJP leader Yashwant Sinha demanded that no talks should be held with Pakistan till the culprits of Mumbai terror attacks and the prime conspirator Saeed were handed over to India by Islamabad.
Maintaining that Malik's statements during the visit had "hurt the prestige of the country", he attacked Shinde for not countering his Pakistani counterpart and remaining "silent" during the entire period.
In the Rajya Sabha, BJP deputy leader Ravi Shankar Prasad said it was "a deliberate design" by Pakistan not to take action against Saeed as he enjoyed "the protection of the Pakistan government", adding that this was "very disturbing".
He charged Shinde with being "conspicuously silent" on many contentious issues raised by Malik during his visit, including that of the Babri Masjid demolition which he termed as "interference in the internal affairs of India."
"If this was to be done, then why was he called," Prasad posed. Later, members in the Upper House sought a discussion on the issue and Rajya Sabha Deputy Chairman P J Kurien agreed to the demand on the "serious" issue.
In his statement, Shinde said he especially mentioned to Pakistan the fact that "our investigations have shown that Hafiz Saeed was one of the masterminds of the 26/11 attack conspiracy and Pakistan has yet to take effective action to charge him."
"I reiterated the value of the voice samples for establishing the identity of those who were audacious to be caught on tape while directing the attackers," he said, adding he also emphasised the need to respond to the Letters Rogatory sent to Islamabad following the investigation by the National Investigation Agency.
Referring to the cases of non-compliance of Red Corner Notices against the absconders of 1993 Mumbai blasts case in which 400 people were killed, the home minister said this was "a blot on our bilateral cooperation in bringing fugitives from law to justice."
"The D-company operatives, led by Dawood Ibrahim, still evade arrest," Shinde said, adding that the United States had recently designated Ibrahim has a "specially designated global terrorist" and another person of his group as "a drug kingpin."