DENVER — Chemicals used to hydraulically fracture rocks in drilling for natural gas in a remote valley in central Wyoming are the likely cause of contaminated local water supplies, federal regulators said Thursday.

The draft report, after a three-year study by the Environmental Protection Agency, represents a new scientific and political skirmish line over whether fracking, as it is more commonly known, poses a threat in the dozens of places around the nation where it is now being used to extract previously unreachable energy resources locked within rock.

The study, which was prompted by complaints from local residents about the smell and taste of their water, stressed that local conditions were unusual at the site, called the Pavillion field, in that the gas wells were far shallower than in many other drilling areas around the country. The shallow depth means that natural gas itself can seep upward naturally through the rock, and perhaps into aquifers.

But the suite of chemicals found in two test wells drilled at the site, the report said, could not be explained entirely by natural processes. The agency’s analysis of samples taken from deep monitoring wells in the aquifer indicated the presence of synthetic chemicals, like glycols and alcohols consistent with gas production and hydraulic fracturing fluids, benzene concentrations well above standards in the Federal Safe Drinking Water Act standards, and high methane levels.