Gandhi was taken into preventative custody after pledging full support to the farmers in villages in Uttar Pradesh state near the capital New Delhi, Press Trust of India news agency reported.
"Rahul Gandhi has been arrested. and will be presented before a sub-divisional magistrate tomorrow," local police inspector general Rajnikant Mishra was quoted as saying.
Gandhi was arrested in a village in Greater Noida, which was cordoned off by police on Monday after deadly clashes with farmers demanding greater compensation from the state government over its land acquisition policy.
"I feel ashamed to call myself Indian after seeing what has happened here. The (state) government here has unleashed atrocities on its own people," he was quoted as telling the protesting farmers before his arrest.
Gandhi, who arrived on a surprise visit riding pillion on a motorbike in the early hours of Wednesday to avoid police deployed there, pledged to support the farmers.
The rising political star is the great grandson of India's independence prime minister Jawaharlal Nehru and son of late former premier Rajiv Gandhi and Italian born Sonia Gandhi, who is head of the national ruling Congress party.
Uttar Pradesh, India's most populous state, is controlled by the regional Bahujan Samaj Party.
The Hindustan Times said Gandhi's visit had "further aggravated simmering tension between the state and central government."
Two policemen and a farmer were killed at the weekend near a suburb of Noida in violent protests against farmland designated for the new motorway.
The Uttar Pradesh state government said the farmers had been given generous compensation.
The villages of Bhatta and Parsaul close to Noida, a prosperous suburb of the capital, were surrounded by police to prevent a rally by opposition politicians.
Land acquisition for roads, factories or other development is a controversial issue across India, with violence often erupting between farmers and police.