The warning comes after council education chiefs ordered tests into reports that the water from the taps was running blue.
North Lanarkshire Council admitted the alarm was first raised three years ago but tests were only ordered in October.
Experts say high levels of copper in corroded pipework can cause the blue colour.
Staff and pupils at both schools have been warned not to drink from the taps and the replacement of hundreds of metres of pipework in the school is being considered.
Buchanan High is a non-denominational school for pupils with additional support needs.
Advice from the Drinking Water Inspectorate states that blue colour in water is rare, but when it happens it is due to corrosion of copper plumbing and indicates high levels of copper in the water.
He said: “It suggests there is something untoward in the system which needs real investigation.
But consultations with a number of environmental organisations, including SEPA, raised no objections to the school complex being built on the site.
A spokesman for North Lanarkshire Council said the “occasional instances” of blue water from taps at the school is due to “potential corrosion in the pipework creating a copper solution”.
He said: “This has little impact on the quality of the water, although there is discoloration, which understandably, can appear alarming.