Around 800 troops was dispatched to the area on the weekend, as armed gangs of Jats, a group practising Hinduism, stormed a mosque and a village with Muslim residents, the state's principal home secretary R.M. Srivastava said.
State police officer Arun Kumar told reporters 28 people are dead and 90 have been arrested over the deadly clashes in the district where 38 percent of the population is Muslim and the remainder mainly Hindu.
"The situation is currently under control," Mr Kumar said.
Authorities declared a high security alert after clashes between Muslims and Hindus in the state, which has witnessed some of the country's worst religious riots in recent decades.
TV footage showed troops on patrol in riot-hit areas with villagers seeking safety in police stations in the worst-hit Muzaffarnagar district, northeast of the capital New Delhi.
Uttar Pradesh's Chief Minister Akhilesh Yadav called for calm in the state, as television aired footage of injured victims on hospital trolleys.
"No leniency will be shown towards those disturbing peace. District officers have been given a free hand to control the situation," Yadav warned in televised remarks.
A broadcast journalist for the local IBN7 television network and a police photographer were among those killed in weekend violence, the most serious in recent years.
The clashes erupted late Saturday after thousands of Hindu farmers held a meeting to demand justice over the killing of three Hindu men who had protested when a woman was allegedly harassed.
The farmers were attacked as they were returning home, triggering an angry backlash, media reported.
Fighting then broke out in neighbouring villages between Hindus and Muslims with the army stepping in to bring the situation under control.
"They started firing rounds at our homes from the fields and soon they were hurling petrol bombs," a Muslim villager, Iqbal Ansari, told the Indian Express daily.
"My house, my belongings and my life's savings were burned to the ground," he said.
Uttar Pradesh witnessed deadly riots in 1992 following the razing of a mosque by a Hindu mob.
More than 2,000 people -- mostly Muslims -- were killed in unrest after the 16th-century mosque in Ayodhya was demolished in some of India's worst communal clashes.
The recent clashes have triggered speculation political parties are seeking to polarize the state along religious lines ahead of general elections due in 2014.
The state's secular ruling Samajwadi Party has accused leaders of the Hindu nationalist Bharatiya Janata Party (BJP) of fuelling tensions with inflammatory speeches.
A state BJP politician, Hukum Singh, rejected accusations that the party was behind the violence.
"The government has failed on all the fronts... they are now searching for a scapegoat," Mr Singh said.
Senior BJP leader Ravi Shankar Prasad accused the state government of failing to act in time to check the violence.
"The state government has failed miserably in maintaining communal harmony," Mr Prasad said.
The BJP is working to revive its fortunes before the elections by attacking the ruling Congress-led government over a string of corruption scandals.
The national government has warned that India is witnessing a rise in communal violence and that there could be more of such incidents in the run-up to polls.
"Communal violence incidents have increased since last year," federal Home Minister Sushilkumar Shinde said.
"While 410 incidents occurred in the country last year, this year, till now, 451 incidents have taken place."