The ban was brought in last week after tests deemed them to contain "unsafe and hazardous" amounts of lead.
Nestle maintains its noodles are safe but last week began withdrawing them from Indian shops.
On Friday the court ruled that as the noodles are being withdrawn anyway "the question of granting stay... at this stage does not arise".
The judges ordered the food authorities to file their responses to Nestle's petition that the ban be completely revoked in time for a further court hearing on 30 June.
Nestle has argued that the tests that found lead are flawed and inaccurate. It says it has carried out its own tests on over 1,000 batches of Maggi noodles, plus commissioned tests at external labs on a further 600 batches.
"All results indicate that Maggi noodles are safe and well within the regulatory limits established in India," the company said.
The instant noodles arrived in India in 1983 and were until recent developments to be found in corner shops across the country.
A Mumbai court has denied Nestle's request for a stay of the nationwide ban on Maggi noodles in India.