While the letter, or "deficiency memo", is not a rejection of Uber's application, the company will have to resubmit a portion of it to be granted a licence, a government official said.
Uber's services have been banned since December in New Delhi, when one of its drivers was accused of raping a passenger. The company restarted operations last week after applying for a radio taxi licence, though the government said Uber was still blacklisted.
In new rules set by New Delhi's transport department last month, taxi-hailing app companies need to install emergency buttons in their cabs and have tracking devices linked to call centres to obtain a licence.
The memo from the transport department seen by Reuters said Uber did not provide details of its call centre and its application lacked proof of its registered office in New Delhi.
"As an applicant, Uber has to come back if it is interested," said a senior transport official who was not authorised to speak with media on the matter and so declined to be identified.
"Otherwise, the application won't move forward... We are not using the word rejected anywhere."
Similar letters were sent to Uber's local rivals TaxiForSure and Ola, which is backed by Japan's SoftBank Corp. The apps of all three firms are currently working in the city.
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TaxiForSure did not respond to a request for comment, while Ola declined to comment. An Uber spokesman said the company is working with authorities to understand their requirements.
Several companies in New Delhi offer taxi services primarily via a smartphone app, but the transport department said some are openly flouting rules and are not registered to ply on roads.
The rape accusation in December reignited debate about women's safety in India and particularly in New Delhi, which is often dubbed India's rape capital.
Uber is also fighting bans in France, Spain and South Korea for alleged violations including using incorrectly licenced drivers. It has also had to contend with further rape allegations against drivers in Chicago and Boston.