The pipeline had to go through a Muslim burial ground in Tiljala.
On Thursday morning, about five members reportedly from the Trinamool Congress gathered at the ground and began to protest against it.
They also allegedly infuriated some people who had come for a burial ceremony, and attacked the workers engaged in the work.
Bibhash Maity, chief engineer, Water Supply, of the KMC, said they had taken a prior permission from the board looking after the burial ground to lay the pipeline. "The work was stopped for a brief period. It resumed in the evening," Maity said.