The new charge was revealed when Clark was arraigned in a Connecticut courtroom where he pleaded not guilty to both the original murder charge and the new charge of felony murder.
Felony murder is defined under Connecticut state law as a homicide that occurs during a felony offense, such as rape or kidnapping. Under the law, prosecutors do not have to prove that a killing was intentional.
Details of what the alleged felony was that Clark was allegedly committing that led to Le's murder were not mentioned during the hearing.
In Clark's arrest warrant released in November, six portions of the text were ordered to remain redacted by the judge, who said they contained information he determined was "inflammatory" and "unfairly prejudicial to the defendant" and that the public did not need to see.
Calls made to the prosecutor's office regarding the felony murder charge by ABCNews.com were not immediately returned.
Clark, 24, appeared in the New Haven Superior Court clad in an orange jumpsuit and with his arms cuffed behind his back and his legs restricted in chains.
His hair neatly coiffed, Clark said little at the hearing, during which he waived his right to a probable cause hearing. Clark made one of his few public comments when Judge Roland Fasano when asked if he understood his rights. "Yes sir, your honor," Clark answered.
A probable cause hearing would have forced prosecutors to prove that they have enough evidence to justify a murder charge against Clark.
It was the fourth time that Clark was brought to court to enter a plea, but each time the plea was delayed over procedural issues.
Le was first reported missing on Sept. 8, when her roommate said she hadn't returned after class. After days of searching, investigators found her body on Sept. 13 - the day she was scheduled to get married - in the Ivy League lab where she worked.
Clark's public defenders, Beth Merkin and Joe Lopez, told ABCNews.com following the brief hearing that their client's mood was "good" and that the hearing "went as expected."
The judge agreed today to allow Clark's mother's car, which had been kept by authorities to test for evidence, to be released.
The next court date is March 3, when the judge will hear arguements about whether to unseal a search warrant issued after Clark's Sept. 17 arrest.
Clark is currently being held at a maximum security prison, the MacDougall-Walker Correctional Institution in Suffield, Conn., on $3 million bail.
Ray Clark Gets Visitors, Cell Mate in Connecticut Prison
Recent reports indicate that Clark receives regular visits from his parents as well as his former fiancee, all of whom often come at night or on the weekends when it is less likely that they get spotted.
According to prison records obtained by Newsday, one jailer described Clark as "nervous," "very respectful," and as one who asks "many questions."
In his own paperwork, Clark writes neatly, according to the paper, that his nickname behind bars is "Ray Ray."
ABC News reported that shortly after Clark was arrested, he was placed on suicide watch and dressed in a garment meant to prevent any suicide attempt.
Newsday cited prison records that state that when he first arrived at jail, Clark was "forced to wear a bulky anti-suicide smock upon intake to being strip-searched multiple times in a single day."
But in recent weeks Clark has been assigned a cellmate and is allowed to go outside for recreation time with other inmates.
In December, an 80-page arrest warrant was released, detailing how the New Haven police found a blood-like substance of the floor of Clark's Middletown, Conn., home. It later tested positive for a presence of blood, but the warrant did not specify whether it matched the DNA of Clark or Le.
Also among the more than 700 items of evidence police obtained while searching Clark's belongings were three cellphones, including an iPhone, a Blackberry and a pink Motorola phone. The ownership of these items was not made clear in the affidavit.
Several pairs of scrub pants, a fishing tackle kit equipped with a fishing line and tackle, as well as white sneakers with unknown "reddish stains" were also found in Clark's car.
Video surveillance from Sept. 8, the day Le is believed to have been murdered, show Clark wearing white sneakers.
Hairs and fibers were also found in Clark's car, according to the warrant.
ABC News' Don Ennis contributed to this report