The company said Tuesday the state Agency of Natural Resources, Public Service Board and Departments of Fish and Wildlife and Public Service have been notified of the "inadvertent removal of harsh sunflowers."
The flowers are considered rare or threatened by the state.
Officials say it happened when contractors were prepping for use of a horizontal directional drill. The drill was supposed to protect the flowers by drilling underneath them.
Vermont Gas says it will complete an investigation and analysis of the impacts before continuing work on the site.
The pipeline currently under construction will extend 41 miles between Colchester and Addison County.