Tear gas and flash bangs could been seen on live streams from the city's streets as police moved to contain large crowds of protestors in tractors and on foot from breaking through barricades.
Many protesters diverted from agreed routes and clashes broke out with police.
Mamata Banerjee said on Tuesday that the Centre's "insensitive attitude" and indifference towards farmers are to be blamed for the violent protests in Delhi, maintaining that she was deeply disturbed by the situation.
"We thank farmers for the unprecedented participation in today's farmers' Republic Day Parade".
By noon, however, certain groups of farmers clashed with the Delhi police at the ITO crossing.
Officials also shut some metro train stations, and mobile internet service was suspended in some parts of the capital.
The government says the reforms will boost rural incomes, while the farmers say they will allow Indian agriculture to be taken over by major conglomerates. They're demanding the repeal of three agriculture laws passed by Modi's government in September that aim to deregulate wholesale produce markets.
Farmers, wearing distinctive colourful turbans, shouted slogans against Prime Minister Narendra Modi and what they called his "black laws".
"We came here for the farmers' support!"
The protests overshadowed Republic Day celebrations, in which Mr Modi oversaw a traditional lavish parade along ceremonial Rajpath boulevard displaying the country's military power and cultural diversity.
Delhi Police Joint CP Shalini Singh said that since morning they had been appealing to farmers to go by pre-approved route but some of them broke police barricades, attacked police personnel. "Local media reported injuries on both sides", the report read. Protesters driving tractors appeared to be deliberately trying to run over police personnel.
Farmers commandeered cranes and used ropes to tear down roadblocks miles from routes approved by the police, forcing constables in riot gear to fall back and let them pass, Reuters witnesses said.
What do the new farming laws propose?
"Agriculture employs more than 40% of India's population but it is a sector plagued by poverty and inefficiency, with farmers often selling their crops for one rupee", it added.
The government's offer to delay the farm laws for 18 months has been rejected by farm leaders, who want a total repeal of the laws.