Thackeray made a series of tweets after migrant workers gathered at Bandra railway station in Mumbai to return to their native states and were later dispersed.
He said migrant labour issue persists everywhere and states and the Centre face a "Catch 22 situation".
"The centre has taken immediate cognisance of the issue and is assisting the state actively. We understand the Catch 22 situation centre and states face. I'm thankful to PM and HM for understanding the situation, while trying to ensure the safety of home states of migrants," he said.
"The migrant labour issue persists everywhere. Even as we house more than 6 lakh migrant labour, with breakfast lunch and dinner, the Union and State Govts are coordinating on further relief for the same. We will continue to ensure the comfort of all migrant labour in our camps," he added.
In his earlier tweets, Thackeray said the issue concerning migrant labour has been repeatedly raised with the Centre which should draw a roadmap to enable them to reach their homes.
He had also referred to incident of "rioting" in Surat.
"The current situation at Bandra Station, now dispersed, or even the rioting in Surat is a result of the Union Government not being able to take a call on arranging a way back home for migrant labour. They don't want food or shelter, they want to go back home," he said.
"Right from the day the trains have been shut down, the State had requested trains to run for 24 hours more so that migrant labour could go back home. CM Uddhav Thackerayji raised this issue in the PM-CM Video Conf as well requesting a roadmap for migrant labour to reach home," he added.
Thackeray said feedback from migrant labour camps has been similar and many were refusing to eat or stay in.
"The law and order situation in Surat, Gujarat, largely has been seen as a similar situation and the feedback from all migrant labour camps is similar. Many are refusing to eat or stay in. Currently more than 6 lakh people are housed in various shelter camps across Maha," he said.
"A mutual road map set by Union Govt will largely help migrant labour to reach home from one state to another safely and efficiently. Time and again this issue has been raised with the centre," he added.
Congress leader Sanjay Nirupam said what happened in Bandra was to happen as migrant labour were not getting food and they are being told not to return to their houses.
"What's happening in Bandra had to happen as they are not getting food and they have been asked not to return to their villages. How long can they stay confined to their small houses? Government relief is just on papers. How many people can be given free food by any government and for how long? Is there no other option?" he said.
BJP leader Kirit Somaiya took a dig at the ruling coalition government over the incident through tweets.
He asked if Thackeray government will explain how people gathered at Bandra railway station.
"What was the Intelligence doing? From where this people come? How sudenly they gather there inspite of 144? Since lockdown never police allow more than 4 person, than how and why today?" he asked.
The 21-day lockdown, which was to end on Tuesday, has been extended till May 3. The lockdown has been enforced to prevent the spread of coronavirus.
( With inputs from ANI )