The former University of Manitoba student awaiting trial in New York on terror-related charges has pleaded not guilty to nine new charges connected to a car bombing attack on a US military base.

Muhanad Al Farekh's lawyer Sean Maher entered the plea in a Brooklyn courtroom Thursday.

The new charges of conspiring to murder U.S. nationals, use of explosives, conspiring to use a weapon of mass destruction and conspiracy to bomb a government facility stem from Al Farekh's alleged involvement in a January 19, 2009 attack on U.S. military base in Afghanistan.

In a release Wednesday, justice officials claimed to have recovered Al Farekh's fingerprints from packing tape of an unexploded car bomb but Al Farekh's lawyer disputes that evidence.

"We are not conceding that the fingerprints that the FBI or various agencies says are Mr. Al Farekh's are actually Mr. Al Farekh's," Sean Maher told the court. "I want that to be clear."

Prosecutors have obtained search warrants for Al Farekh's DNA and are probing deeper into the 2009 attack for evidence people died.

"We have information that there were certain Afghan nationals killed and injured during the course of this attack," Assistant U.S. Attorney  Zainab Ahmad told the court.  "I expect that within the next couple of months, we will know whether or not we have enough evidence to bring death eligible counts in this case."

Ahmad told the court she plans to introduce information gathered under the Foreign Intelligence Surveillance Act into evidence.

Texas-born Al Farekh left Winnipeg for Pakistan with two fellow University of Manitoba students in March 2007. Justice officials say they joined al Qaeda. In 2011, Canada-wide warrants were issued for Al Farekh's companions,  Ferid Imam and Miawand Yar. Their whereabouts are unknown but court documents link Imam to a foiled New York terror plot.

The next court date in the Al Farekh case is set for February 18, 2016.