The Department of Sanitation says the Japanese pagoda sapling died last summer when workers from the Eagle Restaurant Equipment company poured cleaning fluid around its roots.
The sapling had been a replacement for a tree that was chopped down on the Manhattan sidewalk in 1998.
A special office was set up in 2004 to investigate attacks on trees. Someone who kills a tree can face up to a year in jail and a $15,000 fine.
The sanitation department says Eagle Restaurant Equipment has been hit with dozens of citations for noxious liquids, failure to clean and other offenses.
Company owner Penny Chung says her workers never poured anything on the tree but she'll pay the fine.