A 29-year-old man was arrested after he allegedly set fire to two flags at a 9/11 memorial at the Port Authority Bus Terminal, law enforcement sources said.

Jeremias Venegas is accused of burning an American flag and a Port Authority World Trade Center Tribute flag around 11:30 p.m. Sunday at the north wing of the Manhattan terminal, sources told The Post.

Authorities were able to get video of the alleged vandal and he was arrested early Monday morning by Port Authority officers, according to sources.

Venegas was charged with arson and criminal mischief.

Sources said the Port Authority will have a flag raising ceremony Wednesday morning to replace the damaged flags.

The Port Authority lost 84 employees in the 9/11 terror attacks, including 37 who were members of its police department, according to the agency.

“Memorials recognizing September 11 honor the innocent victims and heroes we lost at the hands of a heinous terrorist attack, including 84 members of the Port Authority family,” Port Authority Executive Director Rick Cotton and Chairman Kevin O’Toole said in a joint statement.

“The fact that one of these solemn memorials was so callously desecrated is reprehensible. We applaud the valiant efforts of our PAPD officers for quickly apprehending and arresting the suspect.”

Additional reporting by Tina Moore