The killing of three US citizens, one a 16-year-old boy, in targeted drone strikes last year were unlawful and violated their constitutional rights by not affording them due process, according to a lawsuit filed by their relatives on Wednesday.

Anwar al-Awlaki, a radical Muslim cleric who was placed on a CIA "kill list" last year, died in a targeted strike in Yemen on 30 September that also killed Samir Khan, an alleged propagandist for al-Qaida, in the Arabian Pensinsula. Al-Awlaki's teenage son, Abdulrahman, was killed in a separate strike 200 miles away in which six others died two weeks later.

The lawsuit accuses Leon Panetta, the secretary of defence, David Petraeus, the director of the CIA, and two military commanders of authorising and directing unlawful killings. President Barack Obama is not named in the lawsuit: presidents are immune from civil suits arising from their official actions.

The complaint alleges that the deaths are part of a broader programme of deliberate and premeditated killings by the United States, which rely on "vague legal standards, a closed executive process and evidence never presented to the courts".

The lawsuit has been filed by the American Civil Liberties Union (ACLU) and the Center for Constitutional Rights (CCR) on behalf of Nasser al-Awlaki, the father of Anwar and grandfather of Abdulrahman, and Sarah Khan, the mother of Khan. It aims to force the Obama administration to disclose information about secret decisions behind the killing.

Jameel Jaffer, deputy legal director of the ACLU, said: "It is about accountability. We don't want to minimise the seriousness of the allegations [against Al-Awlaki]. The question here is not whether people are guilty of crimes but whether the government is justified in killing them."

Jaffer said the government had adopted a "dangerous position" over the targeting killing programme by saying that not only do they not have to explain but do not have to acknowledge the killings.

The lawsuit argues that all three killings were unlawful because, outside of military conflict, the constitution and international law prohibit killing without due process, "except as a last resort to avert a concrete, specific, and imminent threat of death or serious physical injury".

Anonymous US government officials were quoted in news reports saying that neither Khan nor Abdulrahman were targets of the strikes that killed them.

The complaint said that if the US government were targeting others, then they failed in their obligations under constitutional and international law to protect Khan, Abdulrahman and "other bystanders".

Pardiss Kebriaei of the CCR said: "The government was quick to claim responsibility for the killing of Anwar al-Awlaki but it said nothing of the strike on the 14 October."

She said there was something "terribly wrong that a 16-year-old boy can be killed by his own government without any explanation".

In a video statement, posted on the ACLU website, Nasser al-Awlaki, said: "I want Americans to know about my grandson. He was a very nice boy he was very caring boy. I never thought that one day this boy, this nice boy, will be killed by his own government for no wrong he did certainly."

It is unclear who the US targeted in the second strike, which was 200 miles away from the strike which killed al-Awlaki. The teenager, who was born in Denver, was killed when he was eating dinner at an outdoor restaurant with his teenage cousin.

Two years ago, ACLU and CCR were unsuccessful in their attempts to involve the courts in an action by Nasser al-Awlaki to try to stop the government from killing his son. A federal judge threw out the case on the basis that Nasser al-Awlaki had no standing to file the lawsuit on behalf of his son. He also said decisions about targeted killings were a "political question" for executive branch officials and not for the courts.

US officials have defended the drone campaign in recent speeches, but the Obama administration has generally refused to openly discuss the criteria for operations.

US government officials, including Eric Holder, the attorney general, have defended targeting suspected terrorists without a trial, even if they are US citizens.

In a speech in March, Holder said: "Some have argued that the president is required to get permission from a federal court before taking action against a United States citizen who is a senior operational leader of al-Qaida or associated forces.

"This is simply not accurate. 'Due process' and 'judicial process' are not one and the same, particularly when it comes to national security. The constitution guarantees due process, not judicial process."

There have been reports that Anwar al-Awlaki was involved in the attempted bombing of a Detroit-bound airliner on Christmas Day 2009 and other terrorist plots, but he was never indicted or tried.