Judge Raymond Dearie ordered Mr Zazi, 24, to be held without bail after prosecutors argued he was a flight risk and "will pose significant danger to the community if released".
The youthful, bearded Mr Zazi, dressed in dark blue and orange prison garb, remained silent during the hearing in federal court in Brooklyn.
Mr Zazi, who before his arrest drove an airport shuttle bus in Denver, Colorado, is accused of preparing a bombing spree in New York this month, possibly on the eighth anniversary of the September 11 attacks.
Prosecutors say he carried bomb-making instructions in a laptop and had been shopping for large quantities of chemicals found in beauty products that could have been the ingredients for explosives.
They also say he received explosives training in Peshawar, Pakistan.
Defence lawyer Michael Dowling said there was no evidence his client had committed a crime. "I would like to stop this rush to judgment," he told dozens of journalists at the courthouse. He said travelling to Pakistan "is not illegal" and that the laptop did not prove any crime had been committed.
The conspiracy charge meant the government's main burden, he said, was to prove Mr Zazi plotted with others.
So far no one else has been charged.
Mr Zazi allegedly drove to New York on September 9 in what a Denver prosecutor called "a chilling, disturbing sequence of events that indicated he intended to make a bomb and intended to be in New York City on 9/11". Prosecutors say Mr Zazi left New York after receiving a tip-off he was being watched by federal agents.
Attorney-General Eric Holder said last week the investigation was continuing.
Source: The Australian