The provincial government media office in a statement said the raid was conducted late on Tuesday night in the vicinity of Khogyani district.
The statement further added that the Special Forces of the Afghan Intelligence, National Directorate of Security (NDS), conducted a night operation in Nakar Khel area of the district on Tuesday night, leaving a Taliban commander and his comrades dead.
Another suspected militant was also arrested during the operation on charges of having links with the anti-government armed militants, the statement said.
The security personnel and local residents did not suffer any casualty during the operation, the provincial government said, adding that some weapons and munitions were also destroyed during the operation.
Nangarhar has been among the relatively calm provinces since the fall of the Taliban regime in 2001 but the anti-government armed militants have been attempting to expand their foothold in this province during the recent years.
However, the Afghan armed forces are busy conducting counter-terrorism operations to suppress the militant groups.