The dramatic arrest of a man in Massachusetts accused of plotting to crash explosive-filled miniature airplanes into the US Capitol and the Pentagon has sparked fresh concerns that the FBI might be using entrapment techniques aimed at Muslims in America.

Rezwan Ferdaus, a 26-year-old US citizen and physics graduate who lived at home with his parents in Ashland, near Boston, was the target of an FBI sting in which he bought a miniature aircraft that he planned to outfit as a flying bomb.

Ferdaus, who is being held without bail, was indicted by a federal grand jury in Boston on Thursday. The six-count indictment – which also covered his alleged efforts to provide support and resources for al-Qaida groups attacking US troops abroad – said he "planned to commit acts of violence against the United States" with the goal of "decapitating" the nation's military center "and killing as many 'kafirs' [non-believers] as possible." A detention hearing has been set for October 3.

However, some legal organisations and Muslim groups have questioned whether Ferdaus, whose activities were carried out with two undercover FBI agents posing as terrorists, would have been able to carry out such a sophisticated plot if left to his own devices. In numerous previous cases in the US, the FBI has been accused of over-zealousness in its investigations and of entrapping people into terror plots who might otherwise not have carried out an attack.

"It deeply concerns us. It is another in a pattern of high-profile cases. Would this person have conceived or executed this plot without the influence of the FBI?" said Heidi Boghosian, president of the National Lawyers Guild.

The Council on American-Islamic Relations also expressed its concern and wondered if more details would later emerge at trial that showed the full scale of the FBI involvement in setting up the sting. "There is a big, big difference between a plot initiated by the FBI and a plot initiated by a suspect, and it seems this might have been initiated by the FBI," said Ibrahim Hooper, CAIR's director of communications.

The lengthy affidavit filed by prosecutors against Ferdaus details an elaborate plot in which he repeatedly expressed his desire to kill Americans and his support for Islamic jihad. The affidavit showed he came up with a detailed plan of attack and even scouted his targets in Washington in person. He also built mobile phone "detonators" that he supplied to undercover FBI agents posing as al-Qaida terrorists and expressed his pleasure when told him they had been used to kill American soldiers in Iraq.

However, the affidavit also raises several questions. Few details are given as to how Ferdaus came to the attention of the FBI. Mention is only made of a co-operating witness, known as CW, who met Ferdaus in December 2010 and soon began recording his conversations.

No details are given as to CW's identity, but it is mentioned that he or she has a criminal record and has served time in prison. That raises the possibility that the CW may have had some ulterior motive to bring an alleged terror suspect to the attention of the FBI or could be an unreliable witness.

Another potential area of concern is a meeting on 19 April 2011, when the undercover agents met with Ferdaus and questioned the "feasibility" of his plan. That raises the prospect that the FBI agents were somehow goading Ferdaus into more action. "Ferdaus responded in a defensive manner that he had made progress," the affidavit stated.

At the same meeting the undercover agents also gave financial assistance for Ferdaus to travel to Washington on a scouting trip: a fact that raises the question of whether he would have made the trip without that financial help. The undercover agents also supplied thousands of dollars in cash for Ferdaus to buy the F-86 Sabre miniature plane to be used in an attack.

Another portion of the affidavit also details Ferdaus's enthusiasm for making mobile phone detonation devices that he believed were being sent to Iraq and used by terrorists. Ferdaus suggested sending a box of 50 mobile phones to war zones where terrorists were in need of them. He even wanted to set up a sort of workshop to produce up to 30 of the devices a week.

"Ferdaus indicated that he could write instructions or make a video on how to construct the cell phone detonation devices," the affidavit said. Such an apparently outlandish idea that hinges on the idea that Islamic terrorists are desperately short of cheap mobile phones might suggest Ferdaus was, to some extent, a fantasist rather than a genuine threat.

However, some legal experts said that the case against Ferdaus appeared compelling, especially as he frequently and repeatedly indicated his desire and willingness to carry out terrorist attacks against Americans. In trying to mount a successful defence of entrapment it is vital to prove that a suspect has no pre-disposition to the crime they are accused of doing. In the Ferdaus case that would seem to be difficult, lawyers said.

"He took the weaponry and agreed to do it. That demonstrates a propensity and willingness to do it," said Anthony Barkow, a former terrorism prosecutor and executive director of the Center on the Administration of Criminal Law at New York University.

Barkow defended the FBI investigation and said that the US authorities took careful steps to avoid the issue of entrapment. "The Justice Department is very aware of this issue," he said.

Certainly the affidavit against Ferdaus paints a compelling picture of a man hellbent on waging jihad in America and eager to take the guns and explosives eventually supplied to him by the undercover FBI agents. He repeatedly states in recorded conversations that he is happy for Americans to die and that the idea for the attack was his own. "That's excellent," Ferdaus said when told one of his phone detonators had been used overseas and had killed Americans.

The prosecution case also reveals how Ferdaus ordered the plane and rented a storage facility in which to keep it and then took delivery from the FBI agents of 25 pounds of C-4 explosives, three grenades and six AK-47 rifles. It also shows Ferdaus explaining how he had become convinced that he needed to attack America after viewing jihadist websites online. "I just can't stop; there is no other choice for me," he said of his decision to launch the attacks.

Prosecutors have staunchly defended the FBI operation. "Our top priority is to protect our nation from terrorism and national security threats," said US attorney Carmen Ortiz.

FBI officials have also said the investigation was carried out responsibly and to head off a real threat. "We have an obligation to take action to protect the public whenever an individual expresses a desire to commit violence. A committed individual, even one with no direct connections to, or formal training from, an international terrorist organization, can pose a serious danger to the community," said Richard DesLauriers, Special Agent in Charge of the FBI's Boston Division