Boston Marathon bombing suspect Dzhokhar Tsarnaev has been cooperating with authorities but can only answer questions by nodding, according to a police spokesman.

Tsarnaev, 19, was being questioned in hospital by detectives. He cannot speak because of a bullet fired through his throat at the end of a massive manhunt that ended on Friday.

Investigators were asking him whether he and his brother Tamerlan, 26, who was killed in a shootout with police, acted alone or had help in the attack that left three people, including an eight-year-old boy, dead and wounded more than 170.

Detectives were interviewing Tsarnaev in his hospital bed at Beth Israel Deaconess Hospital to find out if the brothers had hidden other explosive devices, caches or weapons, a source said.

Tsarnaev was found in a boat beneath a tarpaulin in suburban Watertown after an intensive search by hundreds of police and FBI agents. It is not clear if Tsarnaev was injured by officers in the firefight that erupted on his discovery or inflicted the wound himself.

In hospital, where the FBI said he was in serious but stable condition, Tsarnaev was also visited by a magistrate and prosecutors who laid formal charges against him.

"There has been a sealed complaint filed," Gary Wente, circuit executive for the US Courts for the First Circuit, said.

Tsarnaev has been charged with conspiring to use weapons of mass destruction, the US attorney's office in Massachusetts said. If convicted he could face the death penalty.

The White House has ruled out trying him as an enemy combatant in a military tribunal.

"Under US law, United States citizens cannot be tried in military commissions. It is important to remember that since 9/11, we have used the federal court system to convict and incarcerate hundreds of terrorists," White House spokesman Jay Carney said.

Born in southern Russia, Tsarnaev became a naturalised US citizen in 2012. His father, Anzor Tsarnaev, is due to arrive in the US from Dagestan.

He said he would be seeking "justice and the truth" and had "lots of questions for the police." Both he and his wife Zubeidat Tsarnaeva have claimed their sons had been framed and had nothing to do with the Boston bombing.

They want to take the body of Tamerlan back to Russia for burial.