Officials admitted that the killings had once again endangered the fragile peace in the region.
Another incident - stabbing and then shooting of a couple at Phugana in Shamli district late Wednesday night - fuelled the tension.
Chief Minister Akhilesh Yadav has sent state police chief Deo Raj Nagar to the violence hit region.
Nagar along with Inspector General of Police (Law and Order) R.K. Vishwkarma, who were in New Delhi to participate in a meeting called by the Election Commission of India, are now camping in Muzaffarnagar.
Confirming that the second case involving a couple, where the woman was first stabbed and then shot dead while her husband was critically injured, appeared to be communal in nature, Vishwakarma told IANS that investigations were on to identify the assailants and ascertain the motive behind the attack.
The incident took place on the Hasanpur-Lisadh road when the couple was returning from a doctor. They were intercepted by a group of armed assailants who first stabbed them and then shot at them, injured Rajendra told the police.
He also said that his wife Reena was killed on the spot.
Irate villagers kept the woman's body on the road and blocked traffic, demanding the arrest of the assailants.
Police worry that the agitation by villagers, also supported by the Khap Panchayats, could turn violent in the coming days.
Peace in Muzaffarnagar was shattered Wednesday evening as communal clashes between two groups left three people dead.
The incident took place in Bhaurankalan police station area when people from two communities fought a pitched battle in which three youngsters were shot dead.
The youngsters belonged to Hussainpur Kalan village.
Police reinforcements have been rushed to the area and officials said that all the three dead were Muslims.
District officials also added that retired army man Rajendra Singh told the police that he was working in his field when a group of Muslim youth attacked him. He subsequently raised an alarm and villagers rushed to his rescue.
They later opened fire and in the gun battle that ensued, three youth were killed, the official said.
He added that Rajendra Singh's claims were being ascertained.
The retired army man is a resident of Mohammadpur Raisingh village.
Two people, Arvind and Sharnu of Rajendra Singh's family, have been detained.
Communal riots in Muzaffarnagar and neighbouring areas of Shamli and Meerut had left 63 people dead between Sep 6 and 10. More than 43,000 people were rendered homeless and many of them have refused to go back home, citing the possibility of revenge attacks.
The state government has released Rs.90 crore for the 1,800 families, mostly Muslim, who had refused to go back to their homes.