The incident happened on Wednesday during the countrywide protest strike called by 10 central trade unions and other independent labour associations.
The four arrested in the state all hail from Pulimkunnu near Kottayam and allegedly stopped Levitt's houseboat from moving forward.
This incident has generated lot of negative for the state, as the Centre of Indian Trade Unions (CITU) leaders had assured the state government that the tourism industry had been exempted from the nationwide protest strike call.
On Thursday, as he was leaving the tourist centre, the 72-year-old 2013 Nobel laureate told the media that Kerala is a beautiful and wonderful place without saying a word about his interrupted houseboat journey.
Earlier on Thursday, the Alappuzha District Collector M. Anjana came to meet Levitt and his family to express her deep regret about the events of Wednesday.
The Kottayam District Collector P.K. Sudheer Babu also came and met Levitt in this regard.
Chief Minister Pinarayi Vijayan had earlier directed the two high-ranking officials to convey the state's apologies to the Nobel winner for his work in chemistry.
Levitt, along with his wife had started the Wednesday's journey from Kumarakom in the morning, but, around 11 a.m, their boat was stopped from plying by those taking part in the protests.
It was only two hours after the boatmen informed the authorities of the stoppage that Levitt and his wife could resume their journey and return later to Kumarakom.
( With inputs from IANS )