A bench headed by Chief Justice J S Khehar directed Kerala Water Authority to bear the cost of Rs 28 lakhs cost on cleaning of drainage, sewage and construction debris from the temple premises.
"Given the importance of the issue Kerala Water Authority without tendering will commence work on its own to ensure that the project is completed before the onset of monsoon by May 15, 2017 and the report be fortnightly submitted to the amicus curiae about the work done," the bench also comprising Justices D Y Chandrachud and Sanjay Kishan Kaul said.
The bench said that the committee of administrators can invite the offers separately and can start the process of inviting the expression of interest in a week.
The court posted the matter for further hearing on April 17.
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Senior advocate Gopal Subramaniam, who is assisting the court as amicus curiae in the matter, highlighted the issue and said that restoration work of roof of sanctum sanctorium and of diety is urgently needed.
"disturbing features" and "extremely serious" issues which required immediate redressal over the controversy of alleged mismanagement of the temple.
Subramaniam had earlier in his report highlighted several serious irregularities in the management of the temple and its wealth.
He said physical condition of the temple was pathetic and broken idols measuring two kg were found in plastic bags and cleaning of temple was necessary.
In his 577-page report, Subramaniam had earlier sought an order for audit of the wealth of the Sree Padmanabha Swamy temple by former Comptroller and Auditor General of India Vinod Rai.
The apex court had appointed an expert committee for scientifically documenting the temple's treasure.
The panel comprises experts from ISRO, the Centre for Development of Advanced Computing (C-DAC), the Centre for Earth Sciences Studies and top officials of the Kerala Police.
The sprawling temple, an architectural splendour in granite, was rebuilt in its present form in the 18th century by the Travancore Royal House which had ruled southern Kerala and some adjoining parts of Tamil Nadu before integration of the princely state with Indian Union in 1947.