Shinde has told NDTV channel that hours before the violence erupted on Saturday, he had telephoned Yadav and warned him that "the situation is tense."
He said alerts had been passed on as well.
However, Shinde made it clear that he did not want to accuse the UP government of any failure.
Shinde earlier said this year the number of cases of communal disturbances have gone up in Uttar Pradesh.
"I have spoken to UP chief minister and told him to make necessary arrangements," Shinde said.
The home ministry has asked Uttar Pradesh government to send a report on the situation in Muzaffarnagar every 12 hours.
Meanwhile, Minority Affairs Minister K. Rahman Khan has appealed to the people of the north Indian state not to fall prey to the designs of communal forces.
In a statement here on Monday, he said, "The recent communal violence spread in some parts of Western Uttar Pradesh particularly, district Muzaffar Nagar and its adjoining areas, is a matter of serious concern. I appeal to the people of the State not to fall prey to the designs of communal forces. They should maintain peace and calm."
"Supremacy of law should be maintained at all costs and no credence should be given to rumours. We should not succumb to the nefarious designs of those elements who intend to cause communal divide and then take political advantage out of it," he said.
Khan said the Uttar Pradesh government needs to understand the evil design of certain anti-social elements and should take stringent urgent action against all such elements who are involved in these acts of violence; which have claimed many precious lives and caused damage to property.
"When tempers are frayed, there is no point blaming each other; rather the Uttar Pradesh Government should make serious efforts to restore peace," he said.
Meanwhile, the Akhilesh Yadav government on Monday evening announced the setting up of an inquiry commission headed by retired Justice Vishnu Sahai to probe the Muzaffarnagar violence.
The violence claimed one life on Monday even as more than 800 Army soldiers were deployed in Muzaffarnagar since Sunday.
A state of high alert has been declared for the entire state of Uttar Pradesh with soldiers resorting to door-to-door searches in the district of Muzaffarnagar.
The clashes between two communities also claimed the life of a freelance TV journalist on Saturday. Another photographer was beaten to death in a separate incident.
--IBNS (Posted on 10-09-2013)