Phillipos, 19, of Cambridge, Mass., allegedly lied to investigators on two different occasions about whether he removed items from Tsarnaev's dorm room with two other friends on the night of April 18, three days after the bombings killed three people and injured 260 others.
Phillipos denied that he went to the room with Azamat Tazhayakov and Dias Kadyrbayev, exchange students from Kazakhstan, prosecutors allege.
Federal officials said the three men went to the dorm room and took a backpack containing partially emptied fireworks and other items, The Boston Globe reported.
Tazhayakov and Kadyrbayev were indicted Aug. 8 for allegedly taking the backpack from the room and tossing it and other items into a trash bin.
They have pleaded not guilty.
Phillipos' attorneys, Derege B. Demissie and Susan B. Church, said their client will fight the charges against him.
"It is clear that Phillipos had nothing to do with the removal of the backpack or destruction of potential evidence," a statement from the lawyers said.
A court date for his arraignment had not been set. Officials said if he is convicted he faces up to eight years in prison on each of the two counts.
Tsarnaev faces multiple criminal charges.