An article in the Daily Mail earlier this month said that the foundation of the monument- among the seven wonders of the world - had been damaged.
The court has asked the Archaeological Survey of India (ASI), the Uttar Pradesh government and the central government to look into the claims made by the article.
Some of the experts cited in the story later said they had been misquoted. The article said that the river is crucial in moisturizing the wood used in the Taj's foundation, and that the marble monument could collapse soon.
The ASI which began a major facelift for the Taj Mahal in 2007, dismissed the dire predictions for the 358-year-old monument.
"We have been having regular tests conducted and agencies including Survey of India have never pointed out such threats to the survival of the Taj Mahal," ASI's chief archaeologist in Agra, I.D. Dwivedi, told AFP.
Agra's Member of Parliament Ramshankar Katheria denied forecasting a collapse within five years but he told AFP that he had conveyed his fears for the future of the Taj to Indian Prime Minister Manmohan Singh and President Pratibha Patil more than once.
"I am demanding a high-level enquiry to analyse the severe threat posed to the wooden structures in the foundation of the Taj," the MP said.
He warned that the supporting timber was turning brittle because the level of Yamuna was declining due to the over-extraction of water by residents and businesses.
"The timber in the plinth of the Taj would soon corrode and termites could set in unless it quickly finds a source of moisture," Mr Katheria said in an interview.
"The acrid dust from the dry riverbed is also dulling the domes of the Taj and the government must build a barrage across Yamuna to keep its water levels high," Katheria, who belongs to the main opposition BJP party, added.
The Taj, a popular backdrop to photos of tourists in India, was built by Mughal emperor Shah Jahan as a tomb for his beloved empress, Mumtaz Mahal, who died while giving birth to their 14th child in 1631.
The Trapezium Zone after industries was found to be contributing to the monument's yellowing.
It ordered 292 coal-based factories to switch to natural gas or relocate outside the zone by April 30.
(With AFP inputs)