Oscar Morel from Brooklyn was charged with two counts of second-degree murder and two counts of criminal possession of a weapon by New York police, which did not give any motive for the Saturday killing in the borough of Queens.
The charges came hours after hundreds of mourners attended the funeral service for the 55-year-old mosque leader Maulana Alauddin Akonjee, who was respected locally, and his 65-year-old associate Thara Uddin.
Video of the horrific execution-style killing had also shown the brazen crime to be a planned murder following which the killer fled.
Morel was originally arrested Sunday night on charges related to a hit-and-run accident, some five kilometres from the spot of the murders, and the assault of a police officer, NYPD Chief of Detectives Robert Boyce told reporters.
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"We believe, because of the evidence we've acquired thus far, that we strongly believe this is the individual," Boyce said.
Police said witnesses saw his black Chevy TrailBlazer flee the scene of the shooting.
Muslim leaders chanted "We want justice" and sought a stepped up security including installation of CCTV cameras outside mosques in the area following the incident, that has sent a shockwave among the Bangladeshi community in the neighbourhood and prompted concerns over growing Islamophobia.
Mayor Bill de Blasio, among those who paid respects to the slain duo, promised deployment of more police personnel to protect mosques and the Muslim community as he underlined the entire city stood shoulder-to-shoulder with those in mourning.
Authorities had earlier said hate crime was being probed as a possible motive - as demanded by Muslim elders, who have rejected a report that said the killer may have been settling a score in a feud between Muslims and Hispanics.
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