He met handed over a cheque of Rs 50 lakh along with the appointment letter for the post of 'Vishesh Karyadhikari Kalyan' (Officer on Special Duty) to the slain SP's widow Archana Dwivedi.
The Chief Minister also assured all possible help from the government to the family.
After meeting the family, Akhilesh told reporters that the single-member commission will not only bring out the truth, "but those found guilty will get stringent punishment".
Asserting that his government was not "hiding" anything as its intentions were "clear", he said the commission would take into account all the facts and other related aspects of the incident.
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Twenty-nine people including City Superintendent of Police Mukul Dwivedi and Farah police station officer Santosh Yadav were killed in clashes during a drive to evict illegal occupants of Jawahar Bag in Mathura by activists, believed to be of Azad Bharat Vidhik Vaicharik on June 2.
"There were people from Jharkhand and Madhya Pradesh staying in Jawahar Bag. Since they were provided with food and shelter there, they were never told that the land belonged to the government," he said.
Expressing happiness that the high court order of evacuating encroachers was implemented, he said the government's intention of not harming women and children too was honoured.
"The fleeing inmates of Jawahar Bag were assaulted by the residents of Mathura as they were not happy with their conduct," said Akhilesh.
Vriksh Yadav was his relative and so his government had a "soft corner" for them, Akhilesh said "If someone's surname is Singhal, he does not become a relative of (VHP leader) Ashok Singhal. By virtue of Ram Vriksh being a Yadav, he does not become my relative".
Ram Vriksh too was killed during the clashes.
Terming it a "breach of trust", he condemned a sting operation conducted by a television channel involving a few policemen in Mathura.
"It is very easy to conduct a sting operation these days. The government has acted on intelligence report," he said.
"So far, many families have been benefited from the scheme," he said.
Akhilesh was receptive to the suggestion that Jawahar Bag should be renamed after Dwivedi and Santosh Yadav, an SHO who too was killed during the clashes.
He denied BJP's allegation of Hindu migration from Kairana in Shamli district.
"BJP is lying. Most of the people left the village about 10-15 years back, while others left for occupation about 7-8 years back," he said.
Akhilesh regretted for not being able to visit the house of SHO SantoshYadav due to bad weather yesterday, but said he would visit the SHO's family soon.