The FBI's previous contacts with one of the alleged Boston bombers have come under intense scrutiny as questions were raised about whether it missed vital clues that could have prevented the attack, which killed three people and injured more than 170.

The bureau admitted that it had interviewed Tamerlan Tsarnaev in 2011 "at the request of a foreign government", presumed to be Russia, which was concerned that he was a "follower of radical Islam". The FBI said that it did not find any "terrorism activity" and appears not to have had any further contact with him since.

FBI agents were scrambling to review a six-month visit to Russia by 26-year-old Tsarnaev last year, during which he stayed with his father in Dagestan and is reported to have visited the family's ethnic home of Chechnya.

Dzhokhar Tsarnaev Photograph: Corbis

In Boston, special agents trained in the interrogation of high-value suspects were waiting to question the surviving 19-year-old suspect, Dzhokhar Tsarnaev, who remained in a serious condition in hospital on Saturday.

He was brought late on Friday night to Beth Israel Deaconess medical center – the same hospital where earlier in the day his brother Tamerlan died after a shootout with police. The Massachusetts governor Deval Patrick said on Saturday that Dzhokhar was in a serious but stable condition and was "not able to communicate yet".

As questions were raised about how well known the brothers were to federal investigators, their mother, Zubeidat Tsarnaeva, said that the FBI had spoken to the family on multiple occasions. In an interview broadcast by Russia Today before the end of the manhunt on Friday, Tsarnaeva, a naturalised US citizen, said FBI agents had spoken to her in the past.

Tamerlan Tsarnaev. Photograph: AP

"They were telling me that Tamerlan was really an extremist leader and they were afraid of him. They told me whatever information he is getting, he gets from these extremists' sites." Tsarnaeva, speaking from Dagestan, claimed that the FBI were monitoring her son "at every step", and had been "controlling" him for three to five years. She did not give specific dates.

The White House said Barack Obama had spoken to the Russian president, Vladimir Putin, as the manhunt came to an end on Friday. "President Putin expressed his condolences on behalf of the Russian people for the tragic loss of life in Boston," the White House said in a statement.

Obama "praised the close co-operation that the United States has received from Russia on counterterrorism, including in the wake of the Boston attack," the White House said.

'Off the hook'

But there were concerns in Congress that the FBI appeared not to have maintained contact with Tamerlan Tsarnaev. Representative Peter King of New York, a Republican member of the House homeland security committee, asked whether the FBI could have done more. "Did they move too quickly by letting this guy off the hook?" said King, quoted in Newsday. "Should they have looked more carefully?"

People gather at a makeshift memorial for victims near the site of the Boston Marathon bombings a day after the second suspect was captured. Photograph: Mario Tama/Getty Images

With a week-long manhunt for the suspects now over, and Boston getting back to normal following a virtual lockdown of the city on Friday, questions were also being raised about the approach of federal prosecutors to the surviving suspect.

Dzhokhar Tsarnaev was not read his Miranda rights, the process under US law that would have informed him of his right to remain silent, when he was detained. Ordinarily that would mean that any confession would be inadmissible at trial, but Carmen Ortiz, US attorney for Massachusetts, cited a public safety exception that is intended to prevent the public from immediate danger. The exception would allow investigators to question Tsarnaev about possible accomplices or networks that might have conspired in the attacks.

Republican senators Lindsey Graham and John McCain supported the decision not to read Tsarnaev his Miranda rights, and called for him to be classified as an "enemy combatant".

An expansion of the public safety exception to Miranda by the Obama administration is the subject of controversy, and civil rights advocates expressed concern about how it would be applied. The American Civil Liberties Union said the exemptions should not be "open-ended" and that America "must not waiver from our tried and true justice system".

US attorney Carmen Ortiz speaks during a news conference after the arrest of a suspect of the Boston Marathon bombings in Watertown, Massachusetts. Photograph: Matt Rourke/AP

US prosecutors are considering how best to press charges against Tsarnaev, given his medical condition. They might wait for him to recover sufficiently to be taken to the federal courthouse in south Boston, or they might even request a federal judge comes to the hospital to charge him at the bedside. US officials said a special interrogation unit specialised in dealing with high-value suspects were waiting to question him.

On Friday the FBI took two men and a woman in New Bedford, Massachusetts, into custody and are questioning them about their links to Dzhokhar Tsarnaev.

The federal public defender's office in Massachusetts said it has agreed to represent Tsarnaev once he is charged. Miriam Conrad, public defender for Massachusetts, told the Associated Press that he should have a lawyer appointed as soon as possible because there are "serious issues regarding possible interrogation."

Once federal investigators are allowed access to Tsarnaev, they will be keen to quiz him on his connections – in the US, in Dagestan, where his father lives, and Chechnya, where Tamerlan Tsarnaev is thought to have visited last year.

Much of the investigation is likely to focus on the activities of the elder brother. The FBI has revealed that in 2011 Tamerlan was interviewed by its agents at the request of an unnamed foreign government – widely assumed to have been Russia – who asked the bureau to look into whether Tamerlan, then 24, had extremist connections.

In a statement, the FBI said that the foreign government had information that Tamerlan Tsarnaev was a "follower of radical Islam and a strong believer, and that he had changed drastically since 2010 as he prepared to leave the United States for travel to the country's region to join unspecified underground groups".

No evidence of terrorism

In response to the request, the FBI scoured Tamerlan Tsarnaev's telephone records, online history, associations with other people, movements and educational history, and agents interviewed him and his relatives. But the bureau found no evidence of terrorism activity either at home or abroad. It passed on its findings to the foreign government.

According to US travel records, Tsarnaev arrived at Moscow's Sheremetyevo airport on 12 January 2012, returning on 17 July. He spent time in Makhachkala, Dagestan, that summer. "It was 40C and he was wearing these American boots," said Larissa Abakarova, who maintains a shop across the street from the home of the parents of Tsarnaev. "He was stylish, kind, good-looking. I'm in shock."

School number one, which Boston bombing suspect Dzhokhar Tsarnaev attended as a child, in Makhachkala, Dagestan. Photograph: Reuters

A neighbour, Vyacheslav Kazakevich, said the Tsarnaevs' parents would travel regularly between the neighbouring republics of Dagestan and Chechnya, where several relatives live, including an aunt. He said that Tamerlan visited Chechnya, just an hour's drive from Makhachkala, during his trip to Russia in early 2012. "All their roots are there. They had no ties to rebels or to wahhabi," he said, using the accepted Russian term for Islamist fundamentalists.

In the Russia Today interview, the suspects' mother, Zubeidat Tsarnaeva, claimed they had been set up by the FBI. But by Friday evening, the Tsarnaevs had been questioned by the Federal Security Service, sources said. Zubeidat Tsarnaeva shut off her phone and her husband rarely picked his up after that.

At around 6pm on Friday, a relative drove the two away – some said to Chechnya, others to a secret location in Makhachkala. "She was sobbing last night as she left, you could hear it," said the neighbour, Larissa Abakarova. "She was in hysterics."

By Saturday, more than 50 victims of the Boston bombing remained in hospital, with three in a critical condition.