"It is very clear that injustice has happened. Hundred per cent foolproof investigations are not possible in any case. Many people are arrested during investigation, brought before court and some of them are set free. But repeatedly targeting 'some people' is unfair," Khurshid told reporters on the sidelines of a conference organised by an Urdu news channel.
"Subsequent developments indicate that review and rethinking is necessary in the case," he said, apparently referring to the names of right groups cropping up in the bomb attack.
Khurshid said that Union Home Minister P Chidambaram was in touch with Maharashtra Chief Minister Prithviraj Chavan and Union Law Minister Veerappa Moily to take the case to its logical conclusion.
"Union Home Minister is looking after the matter, Chief Minister is in touch with the Home Minister, and Home Minister is in contact with the Union Law Minister over the issue," he said.
Speaking at the conference, Chavan said that the Malegaon blast, in which 36 people were killed and several others injured on September 8, 2006 in the powerloom town in Nashik district, was a painful chapter in Maharashtra's history.
"Malegaon case was a painful chapter in the state history. The arrested accused would get justice," he said.
"The case was given to the CBI after it was demanded by people. After the incident, few things have come up which would be considered," Chavan said, adding that the guilty would be punished and the secular atmosphere of the state will remain intact.
Swami Aseemanand, who was arrested last November for his alleged role in the 2007 Mecca Masjid blasts, had said in his confession recorded before the magistrate, that a right-wing group was responsible for the 2006 blasts, which killed 36 people and injured over 100.