A bench headed by NGT Chairperson Justice Swatanter Kumar said the Department of Irrigation of Delhi and UP would be responsible for carrying out these directions.
"The debris on either side of river Yamuna, if not already removed, shall be removed within 3 weeks," the bench said.
The green panel said the work for rejuvenation of river Yamuna should not be stopped unnecessarily as the pollution is rising daily and any "inaction on part of authorities cannot be tolerated."
The tribunal reconstituted the Principal Committee, formed to see execution of Yamuna cleaning, and included Shashi Shekhar, former secretary of Ministry of Water Resources as special invitee.
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It also convened a meeting of stakeholders including officials from Delhi, Haryana, Himachal Pradesh, and UP government for cleaning and rejuvenation of river Yamuna which will be held on August 8 at 3 pm at NGT.
"In relation to the project report of the second Phase of the Yamuna cleaning, it is submitted that it has already been filed before the tribunal as well as sent to the Principal Committee, Ministry of Water Resources," the bench noted.
The tribunal had earlier asked some northern states to submit a detailed report on rejuvenation and restoration of Yamuna, saying pollution in the river was of serious concern as it was highly contaminated by industrial effluents and sewage.
The NGT had also directed Haryana and Himachal Pradesh Pollution Control Board to jointly conduct a study of water quality and the flow of Yamuna at the point where it enters Haryana, along with the list of industries which are located on the catchment area of the river.
The tribunal had earlier banned open defecation and dumping of waste on the floodplains of the Yamuna and announced an environment compensation of Rs 5,000 for those who violated the order.
The green panel had noted that almost 67 per cent of the pollution reaching the Yamuna would be treated by the two sewage treatment plants (STP) located at Delhi Gate and Najafgarh under the first phase of the 'Maili se Nirmal Yamuna Revitalisation Project 2017'.
The NGT was hearing a plea on the monitoring of implementation of the project.