The man charged over the Pittsburgh synagogue massacre has pleaded not guilty to hate crimes and dozens of other counts, but his new lawyer signalled he might be open to a plea deal.

Robert Bowers, a truck driver who authorities say gunned down 11 people at the Tree of Life Synagogue, appeared in federal court with lawyer Judy Clarke, who expressed hope the case would be resolved without a trial.

She also represented Boston Marathon bomber Dzhokhar Tsarnaev who was sentenced to death.

Prosecutors in Pittsburgh have previously indicated their intent to seek the death penalty against Bowers, but a final decision rests with the US attorney general.

Asked if the government would consider a plea deal that spares Bowers a potential death sentence, US attorney Scott W Brady said: “The defendant is charged with crimes that carry the maximum possible penalty of death. We are committed to seeking justice for the victims and their families in this case.”

Assistant US attorney Troy Rivetti said in court that a trial could last about three weeks, not including any potential penalty phase.

Bowers, who was shackled, said little, giving yes or no answers.

A grand jury on January 29 added 19 counts to the 44 Bowers was already facing. The additional charges include hate crimes, obstruction of religious belief and the use of a firearm during crimes of violence.

Bowers, 46, of Baldwin, Pennsylvania, is accused of targeting worshippers from three Jewish congregations when he attacked on Saturday October 27, during Sabbath services.

Seven people were wounded, including five police officers.

Donna Coufal, a member of the Dor Hadash congregation that occupies space at Tree of Life, said she attended Monday’s arraignment “to bear witness. It’s been a painful time, but we remain strong as a community”.

Investigators say Bowers posted criticism of a Jewish charity on social media before the attack, claiming the Immigrant Aid Society “likes to bring invaders that kill our people”.

Authorities said he raged against Jews as he gunned down his victims, and told investigators “all these Jews need to die”.

Bowers is being held in Butler County Prison, about 35 miles north of the shooting scene.