The move follows the nomination of Hindu hardline politician Yogi Adityanath as chief minister.
Most are owned by Muslims who make up 18% of the state's population.
Mr Adityanath opposes the slaughter and consumption of cows, considered sacred by India's Hindu majority.
Reports say that immediately after taking office, one of his first acts was to instruct police officials to crack down on "illegal" slaughterhouses in the state.
Locals allege, however, that many of the businesses did not kill cows, but animals like goats and buffalo, the slaughter of which is legal.
India traders fear 'meat crackdown'
They say shops are being shut on technicalities, such as environmental norms. They also say that despite applying for licences they are yet to receive them.
Atul Kumar, a senior official in the state government, earlier told the BBC that the administration was mulling a simplified system to address concerns about granting licences.
Many families say that their livelihoods are at stake, as they have been owning and running these shops for generations.
Chaudhry Iqbal Qureshi, the head of a meat traders association, told BBC Hindi that people were being harassed by authorities which was also why they were striking.
Uttar Pradesh, India's most populous state, is also the largest meat-producing state.
The state government is estimated to earn more than 110bn rupees ($1.7bn; Â£1.3bn) a year from the industry.
Meat traders in the northern Indian state of Uttar Pradesh are on indefinite strike in protest at the closure of butcher's shops and slaughterhouses considered illegal.