The Colombian state-owned utility said the decision followed a spike in the value of ISA's stock.
Protests that have blocked the Pan-American highway since March 12 have caused fuel and food shortages in the southern Colombian departments of Cauca, Nariño and Putumayo, according to officials.
The decision upholds a ruling in November last year in which national hydrocarbons regulator ANLA said the companies provided insufficient information related to water management and contingency plans.
Lopetegui met with Piñera to increase gas exports to Chile
Earlier this month, legislators visited the project site in Acajutla, Sonsonate department.