A bench of Justices M B Lokur and P C Panth said the petitioners, a group of traders from Gujarat, can move NGT for appropriate relief.
The petitioners had moved the apex court for lifting of the interim ban on the thread imposed by the green tribunal on December 14 last year.
The counsel appearing for the traders said the prohibitory orders have been made without even considering the legal provisions.
He said that 'manja' has been used for the threads for decades and there has never been any issue with regard to these posing a threat to humans, animals and birds.
The bench said since the thread is glass-coated, it may be bad for animals and birds.
NGT, while banning the manja last year, said the string, coated with glass and metal powder, poses a threat to the environment.
The green panel had said the ban order would apply to nylon, Chinese and cotton manja coated with glass and directed the Manja Association of India to submit report to Central Pollution Control Board on the harmful effects of kite strings.
The tribunal had earlier issued notices to all state governments and sought their response on the plea of animal rights body 'People for Ethical Treatment of Animals' (PETA) on the matter.
In its petition, PETA has contended that 'manja' posed a grave threat to humans and animals as every year a number of deaths were caused by it.
"To increase the chances of being able to cut as many kites as possible, kite strings are made deliberately sharp with churned glass, metals and other materials in order to make them razor sharp to cut through other persons' kite strings," PETA had said.
'Manja' also posed a huge threat when it came into contact with live overhead electric wires, leading to grid failure, it had said.
"Due to 'manja' being coated with glass, metals and other sharp material, these strings act as good conductors of electricity, increasing the probability of detached manja strings stuck in power lines, electrocuting kite flyers and passers-by coming into contact with these strings," it said.
PETA had averred that minor children were engaged by the cottage industry for the manufacture of 'manja' which caused respiratory problems as they inhaled harmful substances which were extremely detrimental to their health.