Ahmad Khan Rahami, the suspect in the New York-New Jersey bomb plot, has been charged with five counts of attempted murder.

The charges, which also include weapons offences, stem from a gun battle with police in which the 28-year-old naturalised US citizen from Afghanistan was taken into custody.

The FBI said Rahami was wanted in connection with a pipe bomb blast in Seaside Park, New Jersey on Saturday morning and the detonation of a pressure-cooker bomb in Manhattan that evening that injured 29 people.

A second unexploded device was found close to the scene of the New York blast.

Prosecutors say they are still considering charges over those bombings.

On Sunday night, five explosive devices were also found in a bin at a train station in Elizabeth, New Jersey, and Homeland Security officials have told Reuters they believe those devices are linked to the New York bombing.

After being captured on Monday, Rahami was pictured on a stretcher being taken into an ambulance, with a bloodied bandage on his right arm and moving his head from side to side with his eyes open.

Since being detained Rahami, who was not on US anti-terrorism databases, has undergone surgery for a gunshot wound to the leg.

The suspect, who is being held on $5.2m bail, was sleeping in the doorway of a bar when the owner reported him to police. 

An officer went to investigate and recognised him as Rahami.

Police said the man pulled out a gun and shot the officer, who was wearing a bullet-proof vest, in the chest.

A shootout then erupted with other officers before Rahami was captured.

A second officer was injured in the hand in the gun battle in Linden, New Jersey. Both are expected to recover.

New York Mayor Bill de Blasio said officials had every reason to believe the series of blasts "was an act of terror," though investigators said the exact motive was not yet clear. 

Having previously ruled out a link between the Manhattan bombing and international terrorism, New York governor Andrew Cuomo has now acknowledged "it may be foreign-related". 

It has been reported that Rahami travelled to Afghanistan and Pakistan multiple times in recent years, with police considering whether he had been radicalised overseas. 

Citing unnamed law enforcement sources, CNN said the trips included a year-long stay in Pakistan ending in March 2014.

According to the New York Times, no evidence has yet been found that Rahami had military training overseas.

The paper said FBI agents were trying to find out whether his actions had been informed by Islamic State or another such organisation.

US security sources said Rahami had secondary screening after returning from overseas and passed every time. 

Following Rahami's arrest, officials said they had no indication there were more bombs or suspects to find, though they are still investigating. 

Authorities closed in on Rahami after a fingerprint and DNA taken from one of the New York sites and "clear as day" CCTV footage from the bombing scene helped identify him, law enforcement sources told the Associated Press.

Five people were pulled over on Sunday night travelling in a car associated with Rahami, were questioned and released.

Officials said at least one of his relatives was in the vehicle, which appeared to be going towards JFK airport in New York after coming from New Jersey.